Variant report

Variant	rs7697522
Chromosome Location	chr4:48739373-48739374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48737815..48740027-chr4:48780633..48782409,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10003273	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10008265	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10049761	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs10938537	0.95[JPT][hapmap]
rs11737677	1.00[JPT][hapmap]
rs11939889	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11943219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504699	1.00[YRI][hapmap]
rs12512637	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12641022	0.82[EUR][1000 genomes]
rs13113370	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13119041	1.00[JPT][hapmap]
rs13119414	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13141523	0.81[CEU][hapmap]
rs13141838	0.87[EUR][1000 genomes]
rs13142540	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1507865	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1517674	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1554256	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1554258	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1589107	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16861510	0.83[YRI][hapmap]
rs1702798	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1712767	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1712772	0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs17575720	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs17656040	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17656094	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1876469	1.00[JPT][hapmap]
rs1980193	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2056201	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2102397	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs2176460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2289065	1.00[YRI][hapmap]
rs2354314	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2354348	0.95[JPT][hapmap]
rs2354938	1.00[YRI][hapmap]
rs2572345	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2572350	0.89[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs2712156	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2712157	0.81[EUR][1000 genomes]
rs2712158	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2712159	0.82[EUR][1000 genomes]
rs28470767	1.00[JPT][hapmap]
rs28733443	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2883562	0.82[EUR][1000 genomes]
rs2940324	0.83[EUR][1000 genomes]
rs4536901	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4694906	0.90[CEU][hapmap];0.96[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4695391	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4695397	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695400	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695407	0.82[CHB][hapmap]
rs57797824	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62309747	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6447651	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6447655	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447660	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6814811	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6830078	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6830848	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6843340	1.00[JPT][hapmap]
rs6853588	0.85[EUR][1000 genomes]
rs7657332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7657698	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7660206	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7665209	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs7667288	1.00[JPT][hapmap]
rs7670939	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7679210	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs7680280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7681070	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682859	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7683398	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs7693461	1.00[JPT][hapmap]
rs776584	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs776588	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs776591	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs776602	0.85[YRI][hapmap]
rs796555	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs9291326	0.82[CHB][hapmap]
rs937888	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs937889	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs952289	1.00[JPT][hapmap]
rs955683	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9790336	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9997920	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1792683	chr4:48686817-48764009	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1795181	chr4:48686817-48764009	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	esv1792281	chr4:48719424-48764009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1794245	chr4:48719424-48764009	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1794757	chr4:48719424-48764009	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7697522	SLC10A4	cis	lung	GTEx
rs7697522	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48730200-48741200	Weak transcription	Thymus	Thymus
2	chr4:48730200-48744400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:48731600-48744000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:48731600-48751000	Weak transcription	Lung	lung
5	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:48736600-48739400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:48736800-48741400	Weak transcription	Primary T cells from cord blood	blood
8	chr4:48738000-48746800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr4:48738200-48739600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:48738200-48740200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr4:48738200-48740200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr4:48738200-48745400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:48738200-48746600	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr4:48738200-48747000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:48738400-48739400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:48738400-48739400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:48738400-48742600	Weak transcription	HUVEC	blood vessel
18	chr4:48738600-48739600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:48738600-48740400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:48738800-48741000	Weak transcription	Left Ventricle	heart
21	chr4:48738800-48741000	Weak transcription	Pancreas	Pancrea
22	chr4:48739000-48741800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:48739200-48740000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:48739200-48740600	Weak transcription	Primary T cells fromperipheralblood	blood

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