Datasets:

bolinas-dna
/

evals_complex_traits

chrom stringclasses 12 values	pos int64 785k 247M	ref stringclasses 4 values	alt stringclasses 4 values	label bool 2 classes	subset stringclasses 8 values	match_group int64 0 1.33k	rsid stringlengths 3 15	pip float64 0 1	traits stringclasses 191 values	MAF float64 0 0.5	ld_score float64 1.63 1.02k	consequence stringclasses 9 values	consequence_cre stringclasses 23 values	exon_dist int64 0 1.68M	exon_closest_gene_id stringlengths 15 15	tss_dist int64 11 1.68M	tss_closest_gene_id stringlengths 15 15	consequence_final stringclasses 25 values	consequence_group stringclasses 8 values	tss_dist_bin stringclasses 4 values	exon_dist_bin stringclasses 2 values	MAF_bin stringclasses 20 values
1	1,129,916	T	C	true	distal	0	rs4072537	0.992915	P	0.319	33.097	intergenic_variant	dELS_flank	13,554	ENSG00000131591	13,554	ENSG00000131591	dELS_flank	distal	NA	NA	b19
1	1,134,070	C	T	false	distal	0	rs61766348	0.000168		0.31386	69.531	intergenic_variant	dELS_flank	17,708	ENSG00000131591	17,708	ENSG00000131591	dELS_flank	distal	NA	NA	b19
1	2,293,397	G	A	true	distal	1	rs12743493	0.99993	Height	0.37057	32.302	intron_variant	dELS	9,580	ENSG00000157933	65,077	ENSG00000157933	dELS	distal	NA	NA	b19
1	2,299,360	T	C	false	distal	1	rs10797419	0.002939		0.3705	36.621	intron_variant	dELS	3,617	ENSG00000157933	71,040	ENSG00000157933	dELS	distal	NA	NA	b19
1	3,080,038	T	C	true	distal	2	rs1569419	0.999895	MCH,MCV,Plt,RBC	0.23272	31.606	intron_variant	dELS	10,741	ENSG00000142611	10,826	ENSG00000142611	dELS	distal	NA	NA	b19
1	3,408,930	T	C	false	distal	2	rs12065021	0.00045		0.23458	33.993	intron_variant	dELS	2,453	ENSG00000142611	12,438	ENSG00000142611	dELS	distal	NA	NA	b19
1	3,463,266	G	A	false	missense_variant	3	rs183210126	0.000746		0.004938	5.4647	missense_variant	missense_variant	0	ENSG00000130762	2,738	ENSG00000130762	missense_variant	missense_variant	NA	NA	b8
1	3,473,193	A	G	true	missense_variant	3	rs41315284	1	eGFRcys	0.004783	2.4413	missense_variant	missense_variant	0	ENSG00000130762	1,568	ENSG00000130762	missense_variant	missense_variant	NA	NA	b8
1	3,774,926	G	A	false	distal	4	rs6673829	0.000174		0.33868	102.4	intron_variant	dELS	372	ENSG00000235169	2,100	ENSG00000235169	dELS	distal	NA	NA	b19
1	3,774,964	A	G	true	distal	4	rs1175550	0.999975	Hb,HbA1c,MCHC,RBC	0.23057	95.317	intron_variant	dELS	334	ENSG00000235169	2,138	ENSG00000235169	dELS	distal	NA	NA	b19
1	8,447,713	G	A	true	distal	5	rs11581328	0.9903	Height	0.20899	147.54	intron_variant	dELS_flank	9,412	ENSG00000142599	22,500	ENSG00000142599	dELS_flank	distal	NA	NA	b19
1	8,509,422	A	G	false	distal	5	rs200065401	0.000116		0.21593	151.42	intron_variant	dELS_flank	746	ENSG00000142599	16,516	ENSG00000142599	dELS_flank	distal	NA	NA	b19
1	9,295,877	G	T	true	distal	6	rs9442514	0.99332	DVT	0.26506	46.307	intron_variant	dELS	1,282	ENSG00000171621	1,348	ENSG00000171621	dELS	distal	NA	NA	b19
1	9,360,482	C	G	false	distal	6	rs4908854	0.000069		0.26399	35.158	intron_variant	dELS	3,896	ENSG00000171621	4,774	ENSG00000171621	dELS	distal	NA	NA	b19
1	10,591,403	C	T	true	distal	7	rs6540940	0.98386	Balding_Type4	0.0969	56.289	intron_variant	dELS_flank	7,834	ENSG00000142655	53,672	ENSG00000130940	dELS_flank	distal	NA	NA	b16
1	10,594,312	A	G	false	distal	7	rs284271	0.001162		0.09224	67.281	intron_variant	dELS_flank	4,925	ENSG00000142655	50,763	ENSG00000130940	dELS_flank	distal	NA	NA	b16
1	10,611,266	A	G	false	distal	8	rs517344	0.000365		0.05475	69.827	intron_variant	dELS	7,065	ENSG00000142655	33,809	ENSG00000130940	dELS	distal	NA	NA	b15
1	10,630,891	C	T	true	distal	8	rs17035482	0.9969	eGFR,sCr	0.059295	52.934	downstream_gene_variant	dELS	132	ENSG00000142655	14,184	ENSG00000130940	dELS	distal	NA	NA	b15
1	10,692,299	T	C	true	distal	9	rs169537	0.99998	eGFRcys	0.2895	38.555	intron_variant	dELS_flank	1,574	ENSG00000130940	47,222	ENSG00000130940	dELS_flank	distal	NA	NA	b19
1	10,749,494	A	G	false	distal	10	rs416218	0.002669		0.30104	26.198	intron_variant	dELS	11,206	ENSG00000130940	47,151	ENSG00000130940	dELS	distal	NA	NA	b19
1	10,752,360	T	C	false	distal	9	rs205479	0.001305		0.28827	25.736	intron_variant	dELS_flank	8,340	ENSG00000130940	44,285	ENSG00000130940	dELS_flank	distal	NA	NA	b19
1	10,765,520	C	T	true	distal	10	rs11121615	0.99981	Varicose_Veins	0.30847	32.556	intron_variant	dELS	4,662	ENSG00000130940	31,125	ENSG00000130940	dELS	distal	NA	NA	b19
1	12,039,288	A	G	true	distal	11	rs35249183	1	Eosino	0.099751	53.631	intergenic_variant	dELS	7,242	ENSG00000116691	19,789	ENSG00000116691	dELS	distal	NA	NA	b16
1	12,040,885	A	T	false	distal	11	rs71647030	0.00084		0.088348	67.062	intergenic_variant	dELS	8,839	ENSG00000116691	21,386	ENSG00000116691	dELS	distal	NA	NA	b16
1	12,115,601	G	A	true	missense_variant	12	rs2230624	1	Asthma,DVT,Eosino	0.014946	15.876	missense_variant	missense_variant	0	ENSG00000120949	10,297	ENSG00000120949	missense_variant	missense_variant	NA	NA	b11
1	12,138,305	C	A	false	missense_variant	12	rs144498730	0.000076		0.01253	12.789	missense_variant	missense_variant	0	ENSG00000120949	12,405	ENSG00000120949	missense_variant	missense_variant	NA	NA	b11
1	12,186,118	C	T	true	distal	13	rs474247	0.999985	Eosino	0.2179	17.311	intron_variant	dELS	2,677	ENSG00000028137	19,114	ENSG00000028137	dELS	distal	NA	NA	b19
1	12,189,175	T	A	false	distal	13	rs522205	0.000051		0.20324	50.105	intron_variant	dELS	279	ENSG00000028137	22,171	ENSG00000028137	dELS	distal	NA	NA	b19
1	12,601,409	G	C	true	distal	14	rs12136952	0.914735	RBC	0.32957	37.798	intron_variant	dELS	5,100	ENSG00000162496	5,100	ENSG00000162496	dELS	distal	NA	NA	b19
1	12,615,695	G	A	false	distal	14	rs4240903	0.000201		0.32085	36.525	intron_variant	dELS	864	ENSG00000162496	1,099	ENSG00000162496	dELS	distal	NA	NA	b19
1	21,493,549	A	G	true	distal	15	rs12132412	1	Ca,P	0.38873	91.82	intergenic_variant	CA	8,648	ENSG00000142794	15,873	ENSG00000162551	CA	distal	NA	NA	b19
1	21,496,206	A	G	false	distal	15	rs1780323	0.000897		0.4651	93.229	intergenic_variant	CA	11,305	ENSG00000142794	13,216	ENSG00000162551	CA	distal	NA	NA	b19
1	21,564,094	G	A	true	missense_variant	16	rs121918019	1	ALP,P	0.000323	2.1782	missense_variant	missense_variant	0	ENSG00000162551	6,208	ENSG00000162551	missense_variant	missense_variant	NA	NA	b0
1	21,577,454	G	A	false	missense_variant	16	rs34810399	0.00005		0.000048	61.342	missense_variant	missense_variant	0	ENSG00000162551	7,150	ENSG00000162551	missense_variant	missense_variant	NA	NA	b0
1	21,595,639	T	C	true	distal	17	rs55722102	1	P	0.20313	50.995	downstream_gene_variant	dELS	581	ENSG00000076864	24,401	ENSG00000076864	dELS	distal	NA	NA	b19
1	21,608,999	C	T	true	distal	18	rs61775976	0.987	P	0.07792	67.164	intron_variant	dELS	62	ENSG00000076864	11,041	ENSG00000076864	dELS	distal	NA	NA	b16
1	21,648,687	C	G	false	distal	17	rs9426676	0.000167		0.20487	61.094	intron_variant	dELS	1,073	ENSG00000076864	3,148	ENSG00000076864	dELS	distal	NA	NA	b19
1	21,662,952	A	G	false	distal	18	rs72660358	0.00005		0.072863	74.971	intron_variant	dELS	2,258	ENSG00000076864	6,348	ENSG00000076864	dELS	distal	NA	NA	b16
1	22,135,638	T	G	true	distal	19	rs10799737	0.96695	Height	0.34029	161.1	intron_variant	dELS_flank	5,786	ENSG00000162552	5,786	ENSG00000162552	dELS_flank	distal	NA	NA	b19
1	22,153,726	T	C	false	distal	19	rs10917162	0.000926		0.31547	94.731	intron_variant	dELS_flank	9,756	ENSG00000162552	9,756	ENSG00000162552	dELS_flank	distal	NA	NA	b19
1	22,205,049	G	A	true	distal	20	rs79364962	1	eBMD	0.074905	64.635	intergenic_variant	dELS_flank	61,079	ENSG00000162552	61,079	ENSG00000162552	dELS_flank	distal	NA	NA	b16
1	22,219,573	C	A	false	distal	20	rs2807344	0.000119		0.078782	117.47	intergenic_variant	dELS_flank	75,603	ENSG00000162552	75,603	ENSG00000162552	dELS_flank	distal	NA	NA	b16
1	24,914,625	A	G	true	distal	21	rs9438876	0.99947	FEV1FVC	0.48686	31.461	intron_variant	dELS	4,614	ENSG00000020633	15,650	ENSG00000020633	dELS	distal	NA	NA	b19
1	24,941,431	T	C	false	distal	21	rs4649038	0.000415		0.48515	49.058	intron_variant	dELS	11,154	ENSG00000020633	11,154	ENSG00000020633	dELS	distal	NA	NA	b19
1	25,274,256	C	A	true	distal	22	rs139898146	1	MCV,Plt	0.41531	136.34	intron_variant	intron_variant	1,560	ENSG00000187010	1,707	ENSG00000187010	intron_variant	distal	NA	NA	b19
1	25,298,410	G	C	false	distal	22	rs1293267	0.000977		0.48281	221.29	intron_variant	intron_variant	2,535	ENSG00000187010	25,861	ENSG00000187010	intron_variant	distal	NA	NA	b19
1	25,351,114	G	A	true	distal	23	rs72660919	1	HbA1c	0.13313	64.255	intron_variant	dELS_flank	511	ENSG00000183726	12,779	ENSG00000183726	dELS_flank	distal	NA	NA	b17
1	25,356,601	G	A	false	distal	23	rs3093653	0.001031		0.11339	52.256	intron_variant	dELS_flank	191	ENSG00000183726	18,266	ENSG00000183726	dELS_flank	distal	NA	NA	b17
1	25,550,826	G	A	false	distal	24	rs113203593	0.000183		0.040518	42.356	intron_variant	dELS	3,095	ENSG00000157978	7,219	ENSG00000157978	dELS	distal	NA	NA	b14
1	25,551,001	C	T	true	distal	24	rs75446219	0.9999	Plt	0.035202	33.595	intron_variant	dELS	2,920	ENSG00000157978	7,394	ENSG00000157978	dELS	distal	NA	NA	b14
1	26,834,111	G	A	false	distal	25	rs75796628	0.000273		0.028931	36.918	intron_variant	dELS	1,503	ENSG00000204160	2,090	ENSG00000204160	dELS	distal	NA	NA	b13
1	26,853,597	A	C	true	distal	25	rs75460349	0.911215	ALP	0.023521	84.264	intron_variant	dELS	128	ENSG00000204160	3,234	ENSG00000204160	dELS	distal	NA	NA	b13
1	29,159,616	C	T	true	non_coding_transcript_exon_variant	26	rs113292219	0.98168	Ht	0.053917	46.635	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	129	ENSG00000116350	22,265	ENSG00000116350	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	NA	NA	b15
1	29,171,469	C	T	false	non_coding_transcript_exon_variant	26	rs72649258	0.000123		0.056184	70.958	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	10,176	ENSG00000116350	10,412	ENSG00000116350	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	NA	NA	b15
1	33,447,745	G	A	false	distal	27	rs1570685	0.004202		0.31072	205.83	intergenic_variant	intergenic_variant	16,649	ENSG00000134686	16,649	ENSG00000134686	intergenic_variant	distal	NA	NA	b19
1	33,448,732	T	G	true	distal	27	rs11577667	0.90427	Urea	0.32908	132.75	intergenic_variant	intergenic_variant	17,636	ENSG00000134686	17,636	ENSG00000134686	intergenic_variant	distal	NA	NA	b19
1	34,740,329	T	C	false	distal	28	rs476346	0.000048		0.36574	42.57	intron_variant	dELS	14,717	ENSG00000189280	14,717	ENSG00000189280	dELS	distal	NA	NA	b19
1	34,751,775	T	G	true	distal	28	rs585268	1	Height	0.36177	33.024	intron_variant	dELS	3,271	ENSG00000189280	3,271	ENSG00000189280	dELS	distal	NA	NA	b19
1	36,357,766	G	A	false	distal	29	rs758749972	0.000045		0.001164	11.516	intron_variant	dELS_flank	472	ENSG00000196182	3,573	ENSG00000196182	dELS_flank	distal	NA	NA	b2
1	36,367,495	G	C	true	distal	29	rs566921175	0.91173	Neutro	0.001254	3.9405	intron_variant	dELS_flank	352	ENSG00000196182	6,154	ENSG00000196182	dELS_flank	distal	NA	NA	b2
1	36,478,315	C	G	true	distal	30	rs3917932	1	Baso,Neutro,WBC	0.42344	63.613	intron_variant	pELS_flank	1,117	ENSG00000119535	1,203	ENSG00000119535	pELS_flank	distal	NA	NA	b19
1	36,478,453	C	T	false	distal	30	rs3917931	0.000468		0.39399	65.757	intron_variant	pELS_flank	979	ENSG00000119535	1,065	ENSG00000119535	pELS_flank	distal	NA	NA	b19
1	42,849,860	T	C	true	tss_proximal	31	rs56653907	1	Height	0.21972	121.27	intron_variant	pELS_flank	117	ENSG00000164011	304	ENSG00000164011	tss_proximal	tss_proximal	b3	NA	b19
1	42,850,295	G	A	false	tss_proximal	31	rs7520697	0.000648		0.21927	121.51	intron_variant	pELS	363	ENSG00000164011	391	ENSG00000164011	tss_proximal	tss_proximal	b3	NA	b19
1	42,970,380	G	A	true	non_coding_transcript_exon_variant	32	rs841572	0.999465	Ca	0.40667	100.89	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	11,511	ENSG00000117394	11,511	ENSG00000117394	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	NA	NA	b19
1	42,991,474	C	T	false	non_coding_transcript_exon_variant	32	rs9728320	0.000817		0.42705	97.214	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	32,605	ENSG00000117394	32,605	ENSG00000117394	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant	NA	NA	b19
1	45,641,571	C	T	false	distal	33	rs12025613	0.001735		0.30157	805.23	intron_variant	dELS_flank	855	ENSG00000159592	17,516	ENSG00000159588	dELS_flank	distal	NA	NA	b19
1	45,642,819	A	C	true	distal	33	rs11211145	1	Height	0.30156	805	intron_variant	dELS_flank	319	ENSG00000159592	18,764	ENSG00000159588	dELS_flank	distal	NA	NA	b19
1	45,705,721	A	G	false	distal	34	rs28528139	0.00263		0.30327	809.59	intron_variant	CA_flank	5,530	ENSG00000197429	17,539	ENSG00000159596	CA_flank	distal	NA	NA	b19
1	45,706,390	C	T	true	distal	34	rs28370457	1	Height	0.30129	808.05	intron_variant	CA_flank	6,199	ENSG00000197429	18,208	ENSG00000159596	CA_flank	distal	NA	NA	b19
1	46,799,993	T	C	true	tss_proximal	35	rs837402	1	Height	0.05995	93.017	intron_variant	pELS	731	ENSG00000142973	910	ENSG00000142973	tss_proximal	tss_proximal	b4	NA	b15
1	46,800,005	C	T	false	tss_proximal	35	rs837401	0.000032		0.05996	93.019	intron_variant	pELS	743	ENSG00000142973	922	ENSG00000142973	tss_proximal	tss_proximal	b4	NA	b15
1	47,294,986	A	G	false	tss_proximal	36	rs139239408	0.000032		0.033332	27.116	intron_variant	intron_variant	778	ENSG00000123473	861	ENSG00000123473	tss_proximal	tss_proximal	b4	NA	b14
1	47,309,679	G	A	true	tss_proximal	36	rs72686217	1	Height	0.039754	71.648	intron_variant	dELS	596	ENSG00000123473	639	ENSG00000123473	tss_proximal	tss_proximal	b4	NA	b14
1	47,381,796	G	C	false	distal	37	rs17378887	0.000264		0.056317	111.75	intron_variant	dELS_flank	2,956	ENSG00000162368	34,488	ENSG00000186790	dELS_flank	distal	NA	NA	b15
1	47,402,333	C	T	true	distal	37	rs11579058	1	Height	0.062779	91.648	intron_variant	dELS_flank	7,466	ENSG00000162368	13,951	ENSG00000186790	dELS_flank	distal	NA	NA	b15
1	47,449,503	G	T	true	distal	38	rs565692	1	Height	0.41434	184.24	intergenic_variant	dELS_flank	8,811	ENSG00000186564	11,458	ENSG00000186564	dELS_flank	distal	NA	NA	b19
1	47,449,561	A	T	false	distal	38	rs564914	0.004167		0.41413	184.1	intergenic_variant	dELS_flank	8,869	ENSG00000186564	11,516	ENSG00000186564	dELS_flank	distal	NA	NA	b19
1	53,124,129	A	G	true	distal	39	rs1679971	0.99955	Height	0.19722	61.146	intron_variant	dELS	9,155	ENSG00000162383	18,447	ENSG00000162383	dELS	distal	NA	NA	b18
1	53,128,253	T	C	false	distal	39	rs6667002	0.00519		0.18836	76.681	intron_variant	dELS	6,096	ENSG00000162383	14,323	ENSG00000162383	dELS	distal	NA	NA	b18
1	55,050,331	C	A	false	distal	40	rs11206514	0.000072		0.3881	47.076	intron_variant	dELS_flank	1,946	ENSG00000169174	10,035	ENSG00000169174	dELS_flank	distal	NA	NA	b19
1	55,050,515	C	T	false	distal	41	rs11206515	0.000071		0.38766	47.24	intron_variant	dELS	1,762	ENSG00000169174	10,219	ENSG00000169174	dELS	distal	NA	NA	b19
1	55,053,079	C	T	true	distal	40	rs7552841	1	ApoB	0.37639	39.42	intron_variant	dELS_flank	287	ENSG00000169174	12,783	ENSG00000169174	dELS_flank	distal	NA	NA	b19
1	55,053,501	G	A	true	distal	41	rs499883	1	ApoB	0.38525	89.354	intron_variant	dELS	709	ENSG00000169174	13,205	ENSG00000169174	dELS	distal	NA	NA	b19
1	55,232,461	C	T	true	distal	42	rs570635280	0.999995	ApoB,LDLC	0.00145	6.8618	intron_variant	dELS	17,096	ENSG00000162402	17,096	ENSG00000162402	dELS	distal	NA	NA	b2
1	55,233,052	A	C	false	distal	42	rs553533923	0.000038		0.001052	7.844	intron_variant	dELS	17,687	ENSG00000162402	17,687	ENSG00000162402	dELS	distal	NA	NA	b2
1	61,787,811	G	A	false	missense_variant	43	rs3762321	0.000374		0.090499	19.355	missense_variant	missense_variant	0	ENSG00000132849	45,330	ENSG00000132849	missense_variant	missense_variant	NA	NA	b16
1	62,114,219	G	T	true	missense_variant	43	rs12140153	1	ALT,BFP,BMI,BW,Morning_Person	0.095976	65.813	missense_variant	missense_variant	0	ENSG00000132849	128	ENSG00000132849	missense_variant	missense_variant	NA	NA	b16
1	64,838,205	T	C	true	distal	44	rs79649323	0.979785	Eosino	0.015263	12.981	intron_variant	dELS_flank	100	ENSG00000162434	93,109	ENSG00000162437	dELS_flank	distal	NA	NA	b12
1	64,839,141	G	A	false	distal	44	rs150355017	0.000044		0.01901	26.426	intron_variant	dELS_flank	461	ENSG00000162434	94,045	ENSG00000162437	dELS_flank	distal	NA	NA	b12
1	64,848,529	C	A	true	distal	45	rs114269697	0.996295	Eosino	0.013542	19.246	intron_variant	dELS_flank	853	ENSG00000162434	103,433	ENSG00000162437	dELS_flank	distal	NA	NA	b11
1	64,854,838	T	C	false	distal	45	rs61784700	0.000044		0.01231	20.846	intron_variant	dELS_flank	670	ENSG00000162434	109,742	ENSG00000162437	dELS_flank	distal	NA	NA	b11
1	65,487,098	G	A	false	distal	47	rs11808888	0.000899		0.13319	91.043	intron_variant	CA-CTCF_flank	38,590	ENSG00000116678	38,590	ENSG00000116678	CA-CTCF_flank	distal	NA	NA	b17
1	65,516,705	G	A	true	distal	46	rs35660507	0.998835	Age_at_Menarche	0.024817	31.246	intron_variant	intron_variant	8,983	ENSG00000116678	8,983	ENSG00000116678	intron_variant	distal	NA	NA	b13
1	65,516,957	G	A	false	distal	46	rs113407624	0.001004		0.024723	55.852	intron_variant	intron_variant	8,731	ENSG00000116678	8,731	ENSG00000116678	intron_variant	distal	NA	NA	b13
1	65,604,098	A	G	true	distal	47	rs72683129	0.999535	CRP	0.14951	142.19	intron_variant	CA-CTCF_flank	939	ENSG00000116678	38,551	ENSG00000116678	CA-CTCF_flank	distal	NA	NA	b17
1	67,603,891	G	A	false	distal	48	rs1325516	0.000037		0.26906	61.118	intergenic_variant	intergenic_variant	81,309	ENSG00000116717	81,309	ENSG00000116717	intergenic_variant	distal	NA	NA	b19
1	67,622,756	A	G	true	distal	48	rs787488	0.984685	CRP	0.2729	56.7	intergenic_variant	intergenic_variant	62,444	ENSG00000116717	62,444	ENSG00000116717	intergenic_variant	distal	NA	NA	b19
1	68,197,460	C	T	false	distal	49	rs919540	0.001431		0.33296	51.201	intron_variant	dELS_flank	3,232	ENSG00000116729	34,226	ENSG00000116729	dELS_flank	distal	NA	NA	b19
1	68,199,340	T	C	true	distal	49	rs7554551	1	eBMD	0.34494	23.909	intron_variant	dELS_flank	5,112	ENSG00000116729	32,346	ENSG00000116729	dELS_flank	distal	NA	NA	b19

End of preview. Expand in Data Studio

evals_complex_traits

Variant-effect-prediction benchmark of UKBB fine-mapped complex-trait SNVs vs low-PIP SNVs, gene-matched 1:1 within consequence categories and MAF bins.

Description


Positives	UKBB SuSiE+FINEMAP fine-mapped variants with PIP > 0.9 across 119 traits
Negatives	PIP < 0.01 (and not null in any of the 119 traits), gene-matched 1:1 to positives
Genome build	GRCh38 (lifted from hg19 via `liftover`)
Variant type	SNVs only
Coordinates	1-based (`pos` is 1-based; `ref`/`alt` are single bases)

Splits

Split	Variants (positives + matched negatives)	Chromosomes
`train`	1 354 (677 pos + 677 neg)	odd: 1, 3, …, X
`test`	1 304 (652 pos + 652 neg)	even: 2, 4, …, Y
total	2 658

Columns

Column	Type	Description
`chrom`, `pos`, `ref`, `alt`	str / int / str / str	Variant coordinates (1-based, GRCh38)
`label`	bool	`True` for high-PIP positive, `False` for low-PIP matched negative
`subset`	str	Consequence-group label for stratified eval (`distal`, `missense_variant`, `non_coding_transcript_exon_variant`, `tss_proximal`, `3_prime_UTR_variant`, `5_prime_UTR_variant`, `synonymous_variant`, `splicing`)
`match_group`	int	Pos / neg pair ID (every group has 1 positive + 1 matched negative)
`rsid`	str	dbSNP rsID (when available)
`pip`	float	Maximum PIP across the 119 traits
`traits`	str	Comma-separated list of traits with PIP > 0.9 (positives only)
`MAF`	float	UKBB EUR minor allele frequency from the LD-score reference panel
`ld_score`	float	UKBB EUR LD score (passthrough column; not used as a matching feature in this version)
`consequence`, `consequence_cre`, `consequence_final`, `consequence_group`	str	Ensembl VEP consequence + grouping used by the matcher
`exon_dist`, `exon_closest_gene_id`	int / str	0-based half-open distance to nearest protein-coding exon and its Ensembl gene ID
`tss_dist`, `tss_closest_gene_id`	int / str	Same, for nearest protein-coding transcript TSS
`tss_dist_bin`, `exon_dist_bin`, `MAF_bin`	str	Categorical bins used as exact-match keys during gene-matching

Per-subset retention

Subset	Positives kept
distal	1 071
missense_variant	108
non_coding_transcript_exon_variant	50
tss_proximal	43
3_prime_UTR_variant	32
5_prime_UTR_variant	13
synonymous_variant	11
splicing	1
total	1 329

64 % of input fine-mapped SNVs are retained (1 329 / 2 066 — see issue #156). The lower retention vs. mendelian reflects the additional MAF-bin matching constraint that closes a heavy MAF leak in the basic continuous-only design.

Matching design (locked iter24, issue #156)

Splice pre-filter: variants with consequence_group == "splicing" AND exon_dist > 30 are dropped before matching.
Continuous match keys (Euclidean nearest, RobustScaler-scaled): tss_dist, exon_dist, MAF.
Categorical match keys (exact match): chrom, consequence_final, tss_closest_gene_id, exon_closest_gene_id, tss_dist_bin (tss_proximal subset only; edges [0, 50, 100, 200, 500, 1000]), exon_dist_bin (splicing subset only; edges [0, 5, 20, 30]), and an always-on right-closed MAF_bin (20 edges, log-spaced toward low MAF).

ld_score is included as a passthrough column for downstream diagnostics but is not used as a matching feature.

Provenance

Built by the bolinas-dna eval pipeline at commit 3013de3.

Curation pipeline: snakemake/evals/
Matching algorithm: src/bolinas/evals/matching.py
Design discussion: issue #156

The curation is a from-scratch reimplementation of the TraitGym complex-traits pipeline.

Companion datasets

bolinas-dna/evals_complex_traits_harness_255 — same variants with 255 bp reference-genome windows materialized into context / ref_completion / alt_completion columns for direct use as eval-harness inputs.

License

Released under the same terms as its sources. UKBB summary-level data and the Finucane lab fine-mapping release are intended for non-commercial research; check upstream license if you plan to use commercially.

Citation

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

TraitGym — Benegas et al. 2025, bioRxiv 2025.02.11.637758 (songlab-cal/TraitGym)
UKBB fine-mapping — Wang et al. (Nat Commun 2021) and the Finucane lab release
LD scores — Bulik-Sullivan et al. (Nat Genet 2015)

Downloads last month: -