Datasets:

bolinas-dna
/

evals_dsqtl

chrom stringclasses 11 values	pos int64 58.4k 249M	ref stringclasses 4 values	alt stringclasses 4 values	label bool 2 classes	effect float64 -1.96 1.81 ⌀	effect_size float64 0.47 1.96 ⌀	consequence stringclasses 17 values	consequence_cre stringclasses 33 values	exon_closest_pc_gene_id stringlengths 15 15	distance_exon_pc int64 0 1.56M	exon_closest_nc_gene_id stringlengths 15 15	distance_exon_nc int64 0 470k	distance_exon int64 0 470k	exon_closest_gene_id stringlengths 15 15	consequence_final stringclasses 32 values	tss_closest_pc_gene_id stringlengths 15 15	distance_tss_pc int64 0 1.57M	tss_closest_nc_gene_id stringlengths 15 15	distance_tss_nc int64 0 475k	distance_tss int64 0 475k	tss_closest_gene_id stringlengths 15 15
1	906,870	A	G	false	null	null	intron_variant	dELS	ENSG00000187634	17,052	ENSG00000272438	1,912	1,912	ENSG00000272438	dELS	ENSG00000187634	17,052	ENSG00000272438	2,035	2,035	ENSG00000272438
1	910,558	G	A	false	null	null	intron_variant	pELS_flank	ENSG00000187634	13,364	ENSG00000230699	876	876	ENSG00000230699	tss_proximal	ENSG00000187634	13,364	ENSG00000230699	876	876	ENSG00000230699
1	911,109	T	C	false	null	null	intron_variant	pELS	ENSG00000187634	12,813	ENSG00000230699	325	325	ENSG00000230699	tss_proximal	ENSG00000187634	12,813	ENSG00000230699	325	325	ENSG00000230699
1	911,661	C	T	false	null	null	intron_variant	pELS	ENSG00000187634	12,261	ENSG00000230699	187	187	ENSG00000230699	tss_proximal	ENSG00000187634	12,261	ENSG00000230699	225	225	ENSG00000230699
1	914,061	A	G	false	null	null	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000187634	9,861	ENSG00000230699	0	0	ENSG00000230699	non_coding_transcript_exon_variant	ENSG00000187634	9,861	ENSG00000241180	109	109	ENSG00000241180
1	914,991	G	T	false	null	null	intron_variant	pELS	ENSG00000187634	8,931	ENSG00000241180	19	19	ENSG00000241180	tss_proximal	ENSG00000187634	8,931	ENSG00000241180	819	819	ENSG00000241180
1	917,584	T	G	false	null	null	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000187634	6,338	ENSG00000223764	0	0	ENSG00000223764	non_coding_transcript_exon_variant	ENSG00000187634	6,338	ENSG00000223764	949	949	ENSG00000223764
1	921,203	G	A	true	-0.9301	0.9301	upstream_gene_variant	pELS	ENSG00000187634	2,719	ENSG00000223764	186	186	ENSG00000223764	tss_proximal	ENSG00000187634	2,719	ENSG00000223764	186	186	ENSG00000223764
1	928,396	A	C	false	null	null	intron_variant	dELS_flank	ENSG00000187634	1,758	ENSG00000223764	7,379	1,758	ENSG00000187634	dELS_flank	ENSG00000187634	1,915	ENSG00000223764	7,379	1,915	ENSG00000187634
1	931,558	G	A	false	null	null	intron_variant	dELS_flank	ENSG00000187634	468	ENSG00000187634	8,787	468	ENSG00000187634	dELS_flank	ENSG00000187634	1,245	ENSG00000187634	8,787	1,245	ENSG00000187634
1	932,733	G	A	false	null	null	intron_variant	dELS	ENSG00000187634	1,643	ENSG00000187634	7,612	1,643	ENSG00000187634	dELS	ENSG00000187634	2,420	ENSG00000187634	7,612	2,420	ENSG00000187634
1	933,653	C	T	false	null	null	intron_variant	dELS	ENSG00000187634	2,118	ENSG00000187634	6,692	2,118	ENSG00000187634	dELS	ENSG00000187634	3,340	ENSG00000187634	6,692	3,340	ENSG00000187634
1	943,937	C	T	false	null	null	synonymous_variant	synonymous_variant	ENSG00000187634	0	ENSG00000188976	266	0	ENSG00000187634	synonymous_variant	ENSG00000187634	4,661	ENSG00000188976	1,624	1,624	ENSG00000188976
1	956,632	C	T	false	null	null	intron_variant	dELS	ENSG00000188976	261	ENSG00000188976	261	261	ENSG00000188976	dELS	ENSG00000188976	2,623	ENSG00000188976	1,825	1,825	ENSG00000188976
1	966,179	G	A	false	null	null	upstream_gene_variant	pELS	ENSG00000187583	302	ENSG00000187961	1,648	302	ENSG00000187583	tss_proximal	ENSG00000187583	302	ENSG00000187961	2,626	302	ENSG00000187583
1	967,369	C	G	false	null	null	intron_variant	pELS	ENSG00000187583	565	ENSG00000187961	2,838	565	ENSG00000187583	tss_proximal	ENSG00000187583	866	ENSG00000187583	3,505	866	ENSG00000187583
1	976,215	A	G	true	0.6285	0.6285	missense_variant	missense_variant	ENSG00000187642	0	ENSG00000187642	0	0	ENSG00000187642	missense_variant	ENSG00000187583	2,702	ENSG00000187642	425	425	ENSG00000187642
1	986,007	G	A	false	null	null	intergenic_variant	intergenic_variant	ENSG00000187642	3,889	ENSG00000187642	9,365	3,889	ENSG00000187642	intergenic_variant	ENSG00000187642	3,889	ENSG00000187642	9,365	3,889	ENSG00000187642
1	993,218	C	G	false	null	null	intergenic_variant	dELS_flank	ENSG00000188290	5,743	ENSG00000272512	2,747	2,747	ENSG00000272512	dELS_flank	ENSG00000188290	6,762	ENSG00000272512	4,832	4,832	ENSG00000272512
1	995,187	A	G	false	null	null	downstream_gene_variant	dELS_flank	ENSG00000188290	3,774	ENSG00000272512	778	778	ENSG00000272512	dELS_flank	ENSG00000188290	4,793	ENSG00000272512	2,863	2,863	ENSG00000272512
1	995,786	A	G	false	null	null	downstream_gene_variant	dELS	ENSG00000188290	3,175	ENSG00000272512	179	179	ENSG00000272512	dELS	ENSG00000188290	4,194	ENSG00000272512	2,264	2,264	ENSG00000272512
1	1,006,159	C	T	false	null	null	intron_variant	pELS_flank	ENSG00000187608	2,034	ENSG00000231702	1,916	1,916	ENSG00000231702	pELS_flank	ENSG00000187608	5,013	ENSG00000231702	2,069	2,069	ENSG00000231702
1	1,008,332	T	C	false	null	null	intron_variant	PLS	ENSG00000187608	52	ENSG00000231702	102	52	ENSG00000187608	tss_proximal	ENSG00000187608	5,164	ENSG00000231702	102	102	ENSG00000231702
1	1,022,856	T	C	false	null	null	intron_variant	dELS	ENSG00000188157	393	ENSG00000224969	9,662	393	ENSG00000188157	dELS	ENSG00000188157	2,732	ENSG00000224969	9,662	2,732	ENSG00000188157
1	1,045,707	A	G	false	null	null	intron_variant	dELS_flank	ENSG00000188157	25	ENSG00000188157	25	25	ENSG00000188157	tss_proximal	ENSG00000188157	11,600	ENSG00000188157	307	307	ENSG00000188157
1	1,081,817	C	T	false	null	null	downstream_gene_variant	dELS	ENSG00000131591	0	ENSG00000131591	5	0	ENSG00000131591	dELS	ENSG00000237330	7,510	ENSG00000131591	2,254	2,254	ENSG00000131591
1	1,083,795	C	G	false	null	null	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000131591	119	ENSG00000131591	0	0	ENSG00000131591	non_coding_transcript_exon_variant	ENSG00000131591	8,378	ENSG00000131591	276	276	ENSG00000131591
1	1,086,315	A	G	false	null	null	intron_variant	dELS_flank	ENSG00000131591	302	ENSG00000131591	302	302	ENSG00000131591	dELS_flank	ENSG00000131591	5,858	ENSG00000131591	1,320	1,320	ENSG00000131591
1	1,125,786	T	C	false	null	null	intergenic_variant	dELS	ENSG00000131591	9,424	ENSG00000131591	9,542	9,424	ENSG00000131591	dELS	ENSG00000131591	9,424	ENSG00000131591	9,542	9,424	ENSG00000131591
1	1,150,036	T	C	false	null	null	intergenic_variant	dELS_flank	ENSG00000162571	23,843	ENSG00000223823	5,979	5,979	ENSG00000223823	dELS_flank	ENSG00000162571	23,843	ENSG00000223823	13,018	13,018	ENSG00000223823
1	1,153,154	T	C	false	null	null	intergenic_variant	dELS_flank	ENSG00000162571	20,725	ENSG00000223823	9,097	9,097	ENSG00000223823	dELS_flank	ENSG00000162571	20,725	ENSG00000207730	13,949	13,949	ENSG00000207730
1	1,156,085	G	A	false	null	null	intergenic_variant	dELS_flank	ENSG00000162571	17,794	ENSG00000207730	11,018	11,018	ENSG00000207730	dELS_flank	ENSG00000162571	17,794	ENSG00000207730	11,018	11,018	ENSG00000207730
1	1,157,209	G	A	false	null	null	intergenic_variant	dELS	ENSG00000162571	16,670	ENSG00000207730	9,894	9,894	ENSG00000207730	dELS	ENSG00000162571	16,670	ENSG00000207730	9,894	9,894	ENSG00000207730
1	1,159,750	T	C	false	null	null	intergenic_variant	dELS	ENSG00000162571	14,129	ENSG00000207730	7,353	7,353	ENSG00000207730	dELS	ENSG00000162571	14,129	ENSG00000207730	7,353	7,353	ENSG00000207730
1	1,206,007	C	T	false	null	null	intron_variant	pELS	ENSG00000186891	326	ENSG00000186827	5,332	326	ENSG00000186891	tss_proximal	ENSG00000186891	326	ENSG00000186827	7,490	326	ENSG00000186891
1	1,210,386	C	G	false	null	null	downstream_gene_variant	dELS	ENSG00000186827	939	ENSG00000186827	953	939	ENSG00000186827	dELS	ENSG00000186827	3,766	ENSG00000186827	3,111	3,111	ENSG00000186827
1	1,222,167	T	C	false	null	null	intron_variant	dELS	ENSG00000078808	1,076	ENSG00000078808	815	815	ENSG00000078808	tss_proximal	ENSG00000078808	6,428	ENSG00000078808	815	815	ENSG00000078808
1	1,222,251	G	A	false	null	null	intron_variant	dELS_flank	ENSG00000078808	992	ENSG00000078808	899	899	ENSG00000078808	tss_proximal	ENSG00000078808	6,344	ENSG00000078808	899	899	ENSG00000078808
1	1,222,580	T	C	false	null	null	intron_variant	dELS_flank	ENSG00000078808	663	ENSG00000078808	663	663	ENSG00000078808	dELS_flank	ENSG00000078808	6,015	ENSG00000078808	1,228	1,228	ENSG00000078808
1	1,222,640	A	C	false	null	null	intron_variant	dELS	ENSG00000078808	603	ENSG00000078808	603	603	ENSG00000078808	dELS	ENSG00000078808	5,955	ENSG00000078808	1,288	1,288	ENSG00000078808
1	1,226,586	C	A	false	null	null	intron_variant	dELS_flank	ENSG00000078808	1,881	ENSG00000078808	685	685	ENSG00000078808	dELS_flank	ENSG00000078808	2,009	ENSG00000078808	5,234	2,009	ENSG00000078808
1	1,226,734	G	A	false	null	null	intron_variant	dELS	ENSG00000078808	1,733	ENSG00000078808	537	537	ENSG00000078808	dELS	ENSG00000078808	1,861	ENSG00000078808	5,233	1,861	ENSG00000078808
1	1,228,393	C	T	false	null	null	intron_variant	dELS	ENSG00000078808	74	ENSG00000078808	74	74	ENSG00000078808	tss_proximal	ENSG00000078808	202	ENSG00000078808	3,574	202	ENSG00000078808
1	1,228,424	C	T	false	null	null	intron_variant	dELS	ENSG00000078808	43	ENSG00000078808	43	43	ENSG00000078808	tss_proximal	ENSG00000078808	171	ENSG00000078808	3,543	171	ENSG00000078808
1	1,235,869	T	C	false	null	null	downstream_gene_variant	dELS	ENSG00000176022	827	ENSG00000078808	3,837	827	ENSG00000176022	dELS	ENSG00000176022	3,631	ENSG00000078808	3,837	3,631	ENSG00000176022
1	1,238,902	T	C	false	null	null	intergenic_variant	dELS	ENSG00000184163	3,550	ENSG00000184163	3,543	3,543	ENSG00000184163	dELS	ENSG00000176022	6,664	ENSG00000184163	4,255	4,255	ENSG00000184163
1	1,242,864	G	C	false	null	null	missense_variant	missense_variant	ENSG00000184163	0	ENSG00000184163	0	0	ENSG00000184163	missense_variant	ENSG00000184163	3,857	ENSG00000184163	293	293	ENSG00000184163
1	1,246,407	G	A	false	null	null	intron_variant	pELS	ENSG00000184163	106	ENSG00000184163	1,682	106	ENSG00000184163	tss_proximal	ENSG00000184163	314	ENSG00000184163	1,682	314	ENSG00000184163
1	1,246,970	C	T	false	null	null	upstream_gene_variant	PLS_flank	ENSG00000184163	247	ENSG00000184163	2,245	247	ENSG00000184163	tss_proximal	ENSG00000184163	247	ENSG00000184163	2,245	247	ENSG00000184163
1	1,251,122	A	T	true	0.7363	0.7363	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000160087	2,789	ENSG00000260179	0	0	ENSG00000260179	non_coding_transcript_exon_variant	ENSG00000184163	4,399	ENSG00000260179	211	211	ENSG00000260179
1	1,260,213	G	A	false	null	null	intron_variant	dELS	ENSG00000160087	2,902	ENSG00000160087	1,956	1,956	ENSG00000160087	dELS	ENSG00000160087	13,257	ENSG00000160087	3,355	3,355	ENSG00000160087
1	1,274,920	C	G	false	null	null	upstream_gene_variant	PLS	ENSG00000160087	1,064	ENSG00000230415	302	302	ENSG00000230415	tss_proximal	ENSG00000160087	1,064	ENSG00000230415	302	302	ENSG00000230415
1	1,277,886	T	A	false	null	null	intron_variant	intron_variant	ENSG00000162572	2,549	ENSG00000230415	1,181	1,181	ENSG00000230415	intron_variant	ENSG00000162572	2,549	ENSG00000162572	2,585	2,549	ENSG00000162572
1	1,280,469	A	T	false	null	null	5_prime_UTR_variant	5_prime_UTR_variant	ENSG00000162572	0	ENSG00000162572	2	0	ENSG00000162572	5_prime_UTR_variant	ENSG00000162572	32	ENSG00000162572	2	2	ENSG00000162572
1	1,292,032	G	A	true	0.9236	0.9236	downstream_gene_variant	dELS	ENSG00000162572	2	ENSG00000131584	357	2	ENSG00000162572	dELS	ENSG00000162572	4,922	ENSG00000131584	2,975	2,975	ENSG00000131584
1	1,372,258	T	C	false	null	null	intergenic_variant	dELS	ENSG00000175756	1,471	ENSG00000175756	1,985	1,471	ENSG00000175756	dELS	ENSG00000175756	2,898	ENSG00000175756	2,885	2,885	ENSG00000175756
1	1,433,490	C	A	false	null	null	intron_variant	pELS	ENSG00000179403	1,370	ENSG00000225285	687	687	ENSG00000225285	tss_proximal	ENSG00000179403	1,370	ENSG00000225285	997	997	ENSG00000225285
1	1,533,253	C	T	false	null	null	intron_variant	dELS_flank	ENSG00000197785	672	ENSG00000197785	672	672	ENSG00000197785	dELS_flank	ENSG00000205090	7,096	ENSG00000160075	13,233	7,096	ENSG00000205090
1	1,534,092	G	C	false	null	null	3_prime_UTR_variant	3_prime_UTR_variant	ENSG00000197785	0	ENSG00000197785	0	0	ENSG00000197785	3_prime_UTR_variant	ENSG00000205090	6,257	ENSG00000160075	12,394	6,257	ENSG00000205090
1	1,594,618	C	G	false	null	null	intergenic_variant	dELS	ENSG00000228594	3,393	ENSG00000286989	5,695	3,393	ENSG00000228594	dELS	ENSG00000228594	5,516	ENSG00000286989	5,695	5,516	ENSG00000228594
1	1,600,591	C	T	false	null	null	intron_variant	pELS	ENSG00000228594	455	ENSG00000286989	8	8	ENSG00000286989	tss_proximal	ENSG00000228594	455	ENSG00000286989	276	276	ENSG00000286989
1	1,603,213	C	T	false	null	null	downstream_gene_variant	dELS_flank	ENSG00000228594	3,077	ENSG00000286989	509	509	ENSG00000286989	dELS_flank	ENSG00000228594	3,077	ENSG00000286989	2,898	2,898	ENSG00000286989
1	1,607,931	G	A	false	null	null	intergenic_variant	dELS_flank	ENSG00000197530	7,568	ENSG00000286989	5,227	5,227	ENSG00000286989	dELS_flank	ENSG00000197530	7,568	ENSG00000197530	7,522	7,522	ENSG00000197530
1	1,620,609	G	A	false	null	null	intron_variant	dELS	ENSG00000197530	2,779	ENSG00000197530	1,398	1,398	ENSG00000197530	dELS	ENSG00000197530	3,048	ENSG00000197530	2,512	2,512	ENSG00000197530
1	1,631,911	C	T	false	null	null	upstream_gene_variant	PLS_flank	ENSG00000189409	251	ENSG00000189409	266	251	ENSG00000189409	tss_proximal	ENSG00000189409	251	ENSG00000189409	266	251	ENSG00000189409
1	1,685,405	G	A	false	null	null	intron_variant	dELS_flank	ENSG00000189339	5,570	ENSG00000189339	7,043	5,570	ENSG00000189339	dELS_flank	ENSG00000189339	7,318	ENSG00000189339	7,303	7,303	ENSG00000189339
1	1,724,382	T	G	false	null	null	upstream_gene_variant	PLS	ENSG00000008128	24	ENSG00000008128	57	24	ENSG00000008128	tss_proximal	ENSG00000008128	24	ENSG00000008128	57	24	ENSG00000008128
1	1,753,735	C	T	false	null	null	intron_variant	dELS	ENSG00000008130	85	ENSG00000008130	85	85	ENSG00000008130	tss_proximal	ENSG00000008130	3,532	ENSG00000008130	647	647	ENSG00000008130
1	1,753,774	C	G	false	null	null	intron_variant	dELS	ENSG00000008130	124	ENSG00000008130	124	124	ENSG00000008130	tss_proximal	ENSG00000008130	3,493	ENSG00000008130	608	608	ENSG00000008130
1	1,805,214	T	G	false	null	null	intron_variant	dELS_flank	ENSG00000078369	632	ENSG00000078369	632	632	ENSG00000078369	dELS_flank	ENSG00000008130	25,144	ENSG00000078369	11,016	11,016	ENSG00000078369
1	1,864,470	T	C	false	null	null	intron_variant	dELS	ENSG00000078369	24,787	ENSG00000078369	25,231	24,787	ENSG00000078369	dELS	ENSG00000078369	25,930	ENSG00000078369	26,495	25,930	ENSG00000078369
1	1,891,375	G	A	false	null	null	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	ENSG00000078369	257	ENSG00000231050	0	0	ENSG00000231050	non_coding_transcript_exon_variant	ENSG00000078369	257	ENSG00000231050	95	95	ENSG00000231050
1	1,924,659	C	T	false	null	null	intron_variant	CA	ENSG00000142609	138	ENSG00000142609	138	138	ENSG00000142609	CA	ENSG00000178821	5,379	ENSG00000142609	2,743	2,743	ENSG00000142609
1	1,929,687	C	G	false	null	null	intron_variant	CA	ENSG00000142609	372	ENSG00000142609	1,757	372	ENSG00000142609	CA	ENSG00000178821	10,407	ENSG00000142609	1,757	1,757	ENSG00000142609
1	1,942,075	A	G	false	null	null	synonymous_variant	synonymous_variant	ENSG00000142609	0	ENSG00000142609	4,272	0	ENSG00000142609	synonymous_variant	ENSG00000178821	22,795	ENSG00000142609	14,145	14,145	ENSG00000142609
1	1,942,260	G	C	false	null	null	intron_variant	dELS_flank	ENSG00000142609	103	ENSG00000142609	4,087	103	ENSG00000142609	dELS_flank	ENSG00000178821	22,980	ENSG00000142609	14,330	14,330	ENSG00000142609
1	1,947,487	T	A	false	null	null	intron_variant	dELS_flank	ENSG00000142609	432	ENSG00000142609	432	432	ENSG00000142609	dELS_flank	ENSG00000178821	28,207	ENSG00000142609	12,618	12,618	ENSG00000142609
1	1,958,353	A	T	false	null	null	intron_variant	CA-H3K4me3	ENSG00000142609	766	ENSG00000142609	766	766	ENSG00000142609	CA-H3K4me3	ENSG00000142609	32,575	ENSG00000142609	1,752	1,752	ENSG00000142609
1	1,959,717	C	T	false	null	null	intron_variant	dELS	ENSG00000142609	246	ENSG00000142609	246	246	ENSG00000142609	tss_proximal	ENSG00000142609	31,211	ENSG00000142609	388	388	ENSG00000142609
1	1,976,473	C	T	false	null	null	intron_variant	dELS_flank	ENSG00000142609	2,274	ENSG00000142609	2,274	2,274	ENSG00000142609	dELS_flank	ENSG00000142609	14,455	ENSG00000142609	16,364	14,455	ENSG00000142609
1	1,978,114	T	A	false	null	null	intron_variant	dELS_flank	ENSG00000142609	3,915	ENSG00000142609	3,915	3,915	ENSG00000142609	dELS_flank	ENSG00000142609	12,814	ENSG00000142609	18,005	12,814	ENSG00000142609
1	1,987,096	A	T	false	null	null	intron_variant	dELS_flank	ENSG00000142609	60	ENSG00000142609	60	60	ENSG00000142609	dELS_flank	ENSG00000142609	3,832	ENSG00000142609	16,617	3,832	ENSG00000142609
1	2,005,104	A	G	false	null	null	intergenic_variant	CA-H3K4me3	ENSG00000142609	1,266	ENSG00000142609	1,266	1,266	ENSG00000142609	CA-H3K4me3	ENSG00000142609	1,266	ENSG00000142609	1,266	1,266	ENSG00000142609
1	2,019,182	G	A	false	null	null	upstream_gene_variant	PLS	ENSG00000187730	146	ENSG00000187730	177	146	ENSG00000187730	tss_proximal	ENSG00000187730	146	ENSG00000187730	177	146	ENSG00000187730
1	2,021,343	C	A	false	null	null	intron_variant	pELS_flank	ENSG00000187730	1,851	ENSG00000187730	971	971	ENSG00000187730	tss_proximal	ENSG00000187730	1,858	ENSG00000187730	971	971	ENSG00000187730
1	2,031,736	A	G	false	null	null	downstream_gene_variant	dELS	ENSG00000187730	977	ENSG00000187730	994	977	ENSG00000187730	dELS	ENSG00000187730	4,106	ENSG00000187730	2,816	2,816	ENSG00000187730
1	2,033,837	C	T	false	null	null	intergenic_variant	dELS_flank	ENSG00000187730	3,078	ENSG00000187730	3,095	3,078	ENSG00000187730	dELS_flank	ENSG00000187730	6,207	ENSG00000187730	4,917	4,917	ENSG00000187730
1	2,042,324	C	A	false	null	null	intergenic_variant	dELS_flank	ENSG00000067606	8,086	ENSG00000226969	6,878	6,878	ENSG00000226969	dELS_flank	ENSG00000067606	8,086	ENSG00000226969	7,326	7,326	ENSG00000226969
1	2,044,405	C	T	false	null	null	intergenic_variant	dELS	ENSG00000067606	6,005	ENSG00000226969	4,797	4,797	ENSG00000226969	dELS	ENSG00000067606	6,005	ENSG00000226969	5,245	5,245	ENSG00000226969
1	2,067,567	G	A	false	null	null	intron_variant	CA-H3K4me3	ENSG00000067606	5,894	ENSG00000067606	3,731	3,731	ENSG00000067606	CA-H3K4me3	ENSG00000067606	5,894	ENSG00000067606	11,887	5,894	ENSG00000067606
1	2,068,401	C	T	false	null	null	intron_variant	dELS_flank	ENSG00000067606	5,060	ENSG00000067606	2,897	2,897	ENSG00000067606	dELS_flank	ENSG00000067606	5,060	ENSG00000067606	12,721	5,060	ENSG00000067606
1	2,075,464	G	A	false	null	null	intron_variant	pELS_flank	ENSG00000067606	84	ENSG00000067606	3,927	84	ENSG00000067606	tss_proximal	ENSG00000067606	219	ENSG00000067606	6,783	219	ENSG00000067606
1	2,075,725	A	C	false	null	null	intron_variant	pELS_flank	ENSG00000067606	345	ENSG00000067606	4,188	345	ENSG00000067606	tss_proximal	ENSG00000067606	480	ENSG00000067606	6,522	480	ENSG00000067606
1	2,076,945	T	C	false	null	null	intron_variant	dELS	ENSG00000067606	1,565	ENSG00000067606	5,302	1,565	ENSG00000067606	dELS	ENSG00000067606	1,700	ENSG00000067606	5,302	1,700	ENSG00000067606
1	2,079,172	G	A	false	null	null	intron_variant	dELS_flank	ENSG00000067606	3,792	ENSG00000067606	3,075	3,075	ENSG00000067606	dELS_flank	ENSG00000067606	3,927	ENSG00000067606	3,075	3,075	ENSG00000067606
1	2,079,230	A	G	false	null	null	intron_variant	dELS_flank	ENSG00000067606	3,850	ENSG00000067606	3,017	3,017	ENSG00000067606	dELS_flank	ENSG00000067606	3,985	ENSG00000067606	3,017	3,017	ENSG00000067606
1	2,094,081	G	A	false	null	null	intron_variant	dELS_flank	ENSG00000067606	4,265	ENSG00000067606	11,620	4,265	ENSG00000067606	dELS_flank	ENSG00000067606	10,634	ENSG00000067606	11,832	10,634	ENSG00000067606
1	2,096,534	C	T	false	null	null	intron_variant	dELS	ENSG00000067606	1,812	ENSG00000067606	14,073	1,812	ENSG00000067606	dELS	ENSG00000067606	8,181	ENSG00000067606	14,285	8,181	ENSG00000067606
1	2,112,343	C	T	false	null	null	intron_variant	dELS	ENSG00000067606	525	ENSG00000067606	22,918	525	ENSG00000067606	tss_proximal	ENSG00000067606	688	ENSG00000067606	22,918	688	ENSG00000067606
1	2,121,579	T	C	false	null	null	intron_variant	dELS	ENSG00000067606	5,268	ENSG00000067606	13,682	5,268	ENSG00000067606	dELS	ENSG00000067606	5,373	ENSG00000067606	13,682	5,373	ENSG00000067606

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evals_dsqtl

Variant-effect-prediction benchmark of dsQTLs (DNase-seq chromatin accessibility): statistically significant chromatin-accessibility QTLs vs control variants, both within accessible peaks. Sourced from DART-Eval Task 5 and brought into the marin-dna evals pipeline with chromosome-based train/test splits for model development.

No matching and no subsampling — every positive and negative is kept at its natural ratio (≈1:48 positive:negative).

Description


Positives	Significant dsQTLs within accessible peaks (`label = True`)
Negatives	Control variants in peaks, no significant association (`label = False`)
Assay	DNase-seq chromatin accessibility
Source study	Yoruban dsQTLs, Degner et al. Nature 2012
Source data	DART-Eval, Synapse `syn60756039`
Genome build	GRCh38 (lifted from hg19)
Variant type	SNVs only
Coordinates	1-based (`pos` is 1-based; `ref`/`alt` are single bases)
Matching	none (natural class ratio)

Splits

Chromosome-parity split (same convention as the other evals_* datasets).

Split	Variants	Positives	Negatives	Chromosomes
`train`	15,018	309	14,709	odd: 1, 3, …, X
`test`	12,328	250	12,078	even: 2, 4, …, Y
total	27,346	559	26,787

Columns

Column	Type	Description
`chrom`, `pos`, `ref`, `alt`	str / int / str / str	Variant coordinates (1-based, GRCh38). `ref`/`alt` oriented against the reference.
`label`	bool	`True` for a significant dsQTL, `False` for a control variant
`effect`	float	Signed study effect (`obs.estimate`), oriented to the `alt` allele — positive ⇒ `alt` increases accessibility; sign-flipped for variants whose ref/alt were swapped to match the reference, and present for positives only. This is the value the Pearson correlation uses.
`effect_size`	float	Unsigned effect magnitude (absolute value of `effect`).
`consequence`, `consequence_cre`, `consequence_final`	str	Ensembl VEP consequence (raw, with-CRE-class, and after TSS/exon-proximity recategorization); reference annotations
`distance_tss_pc`, `distance_tss_nc`, `distance_tss`	int	Distance to nearest protein-coding / non-protein-coding TSS, and the minimum
`tss_closest_pc_gene_id`, `tss_closest_nc_gene_id`, `tss_closest_gene_id`	str	Ensembl gene IDs at those distances
`distance_exon_pc`, `distance_exon_nc`, `distance_exon`	int	Same shape, for nearest exon
`exon_closest_pc_gene_id`, `exon_closest_nc_gene_id`, `exon_closest_gene_id`	str	Same shape

The consequence/distance columns are reference annotations only — they are not used to match or filter the variant set.

Evaluation

Following DART-Eval Task 5 (§4.5) and ARSENAL, score each variant with a model's allelic effect (e.g. an alt-vs-ref log-likelihood ratio) and report two complementary metrics, each over a different variant set:

Classification — AUROC / AUPRC over all variants: significant dsQTLs (label = True) vs control variants (label = False).
Pearson correlation over the positive variants only (label = True): between effect (signed, oriented to alt) and the model's signed alt-vs-ref score. DART-Eval Table 6: "for the positive variants, we computed the correlation between measured and predicted allelic effects." Controls are not used in the correlation (and for dsQTL they have no measured effect_size).

Provenance

Built by the marin-dna eval pipeline at commit 1c7ec2f.

Curation pipeline: snakemake/evals
Rules: snakemake/evals/workflow/rules/dart_eval.smk
Parsing + annotation: src/marin_dna/pipelines/evals/dart_eval.py

License

Released under the terms of its upstream sources. The variant set is redistributed from DART-Eval (Task 5) and derives from the original QTL study (Yoruban dsQTLs, Degner et al. Nature 2012); DART-Eval ships no explicit license, so consult it and the source study for redistribution and commercial-use terms.

Citation

If you use this benchmark, please cite the upstream sources:

DART-Eval — Patel et al. 2024, arXiv 2412.05430 (NeurIPS D&B 2024)
dsQTL study — Yoruban dsQTLs, Degner et al. Nature 2012

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Paper for bolinas-dna/evals_dsqtl

DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA

Paper • 2412.05430 • Published Dec 6, 2024