Variant report

Variant	rs1879619
Chromosome Location	chr12:103851111-103851112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10128971	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10400501	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10400505	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10400542	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10400543	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10467019	0.90[CHB][hapmap]
rs10467020	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10467024	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10507165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10860994	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10860998	0.81[EUR][1000 genomes]
rs10860999	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10861001	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10861002	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10861003	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861004	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10861020	0.84[EUR][1000 genomes]
rs10861026	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10861028	0.80[EUR][1000 genomes]
rs11111547	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111548	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11111549	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111550	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111568	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111590	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11111594	0.83[EUR][1000 genomes]
rs11111600	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs11111601	0.81[EUR][1000 genomes]
rs11111602	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11111606	0.81[EUR][1000 genomes]
rs11111607	0.80[EUR][1000 genomes]
rs11503454	0.80[EUR][1000 genomes]
rs12227434	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12227436	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12230097	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12230309	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12296693	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12298824	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs12302389	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12304113	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12306102	0.83[EUR][1000 genomes]
rs12306466	0.81[EUR][1000 genomes]
rs12308341	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12309875	0.81[EUR][1000 genomes]
rs12311801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12317094	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12317177	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12319950	0.81[EUR][1000 genomes]
rs12320001	0.81[EUR][1000 genomes]
rs12814770	0.84[EUR][1000 genomes]
rs12815173	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12816735	1.00[CEU][hapmap]
rs12823492	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12825882	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12830978	1.00[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1317388	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1317389	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1317390	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17033809	0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.80[ASN][1000 genomes]
rs17033834	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17033840	1.00[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17033932	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2374046	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2374064	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2374066	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2374071	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs2888734	1.00[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs35045561	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35663013	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35982214	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4015526	0.81[EUR][1000 genomes]
rs7135654	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7139422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7303337	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7303437	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7310675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7956770	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7957584	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7957668	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7972044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1879619	NT5DC3	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103847600-103851400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:103848000-103851400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:103848200-103851800	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:103848400-103851400	Enhancers	GM12878-XiMat	blood
5	chr12:103848400-103851600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr12:103848400-103851800	Enhancers	Primary B cells from cord blood	blood
7	chr12:103848400-103851800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:103848400-103853200	Enhancers	Dnd41	blood
9	chr12:103848600-103851400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr12:103848600-103851800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:103848600-103852200	Enhancers	Primary T cells from cord blood	blood
12	chr12:103849400-103852400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:103850200-103851200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr12:103850400-103851200	Weak transcription	Thymus	Thymus
15	chr12:103850400-103851800	Enhancers	Brain Germinal Matrix	brain
16	chr12:103850800-103852800	Enhancers	Fetal Brain Male	brain
17	chr12:103851000-103851400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr12:103851000-103852000	Enhancers	Fetal Brain Female	brain

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