Variant report

Variant	rs6442119
Chromosome Location	chr3:48440178-48440179
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48438455..48441230-chr3:48472169..48474219,2	MCF-7	breast:
2	chr3:48439572..48442493-chr3:48479629..48481909,2	MCF-7	breast:
3	chr3:48439708..48442673-chr3:48444989..48447626,2	MCF-7	breast:
4	chr3:48289675..48292445-chr3:48439874..48442406,2	K562	blood:
5	chr3:48438011..48440671-chr3:48444874..48447254,2	K562	blood:
6	chr3:48436674..48441480-chr3:48459249..48462395,4	MCF-7	breast:
7	chr3:48341251..48343497-chr3:48440104..48442110,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232112	Chromatin interaction
ENSG00000172113	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000164051	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1037773	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10470686	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109227	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130171	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11712561	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11797	0.82[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12487542	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13069724	1.00[CEU][hapmap];0.97[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs13071337	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13072012	0.91[EUR][1000 genomes]
rs13076076	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs13091785	0.95[EUR][1000 genomes]
rs13314659	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324374	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1459242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1459249	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1459250	0.91[EUR][1000 genomes]
rs1563736	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1870444	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1975844	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045554	0.94[EUR][1000 genomes]
rs2242150	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs2279077	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290822	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2362450	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2362452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28824259	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2885509	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2885510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3214041	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34761139	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35215722	0.92[EUR][1000 genomes]
rs3774808	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4490383	0.93[EUR][1000 genomes]
rs4858793	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858795	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs4858817	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858819	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs56298324	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60512868	0.97[EUR][1000 genomes]
rs6442116	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442117	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442120	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442123	0.94[EUR][1000 genomes]
rs6442124	0.84[EUR][1000 genomes]
rs6764415	0.83[EUR][1000 genomes]
rs6770470	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6776700	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs6779262	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784322	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784541	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794875	1.00[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6796491	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6800475	0.95[EUR][1000 genomes]
rs6804774	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810060	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7126	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs725309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs725310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs730566	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs73074358	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs734071	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs7618883	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7630741	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7634377	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7635522	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636044	0.96[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7636782	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639743	0.91[EUR][1000 genomes]
rs7651407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap]
rs7653691	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs922075	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs9311423	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311424	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311428	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs9809843	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817615	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9826195	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9826247	0.94[EUR][1000 genomes]
rs9838618	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9849509	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs9862575	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864371	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864815	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875280	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876781	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9876891	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9881491	0.95[EUR][1000 genomes]
rs9883759	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9883927	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6442119	CXCR6	cis	parietal	SCAN
rs6442119	TREX1	cis	multi-tissue	Pritchard
rs6442119	SHISA5	cis	lymphoblastoid	seeQTL
rs6442119	SBK1	trans	cerebellum	SCAN
rs6442119	LOC728377	cis	Liver	GTEx
rs6442119	ZNF589	cis	cerebellum	SCAN
rs6442119	ALAS1	cis	parietal	SCAN
rs6442119	AMT	cis	cerebellum	SCAN
rs6442119	BC021960	trans	multi-tissue	Pritchard
rs6442119	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs6442119	TMA7	cis	Muscle Skeletal	GTEx
rs6442119	AMT	cis	parietal	SCAN
rs6442119	TREX1	cis	Liver	GTEx
rs6442119	ZNF589	cis	parietal	SCAN
rs6442119	C3orf18	cis	cerebellum	SCAN
rs6442119	NME6	cis	cerebellum	SCAN
rs6442119	SCOTIN	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48435400-48449800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48437200-48441600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:48439200-48441600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:48439200-48443000	Weak transcription	HUVEC	blood vessel
5	chr3:48439400-48440400	Enhancers	Spleen	Spleen
6	chr3:48439400-48441400	Enhancers	HepG2	liver
7	chr3:48439400-48441600	Enhancers	Pancreas	Pancrea
8	chr3:48439400-48442000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:48439400-48442000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:48439400-48445000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:48439400-48447800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:48439600-48440600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:48439600-48442000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:48439600-48442200	Weak transcription	Brain Germinal Matrix	brain
15	chr3:48440000-48441000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:48440000-48441200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:48440000-48441600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:48440000-48442200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:48440000-48442200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:48440000-48443000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:48440000-48443800	Weak transcription	Lung	lung
22	chr3:48440000-48444000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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