Variant report

Variant	rs7596661
Chromosome Location	chr2:113026189-113026190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113011034..113012645-chr2:113023900..113026719,2	MCF-7	breast:
2	chr2:113020796..113023411-chr2:113025323..113027811,3	MCF-7	breast:
3	chr2:113012358..113014403-chr2:113025508..113027956,2	MCF-7	breast:
4	chr2:113013051..113015199-chr2:113024386..113026807,2	K562	blood:
5	chr2:112990251..112993065-chr2:113025836..113028410,2	K562	blood:

Variant related genes	Relation type
ENSG00000144161	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10864901	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11123133	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11676628	0.85[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs11679986	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11682795	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11685462	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11685514	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11687980	0.87[CEU][hapmap];0.93[GIH][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11688511	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11689858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11691239	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11693294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11695974	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12474447	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12477879	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4516428	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55798617	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55802705	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55821286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55861985	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56044884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56048537	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6542056	1.00[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs6711180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6722612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6747639	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6759283	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6761440	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72831633	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831634	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831636	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831638	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831639	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72831641	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72831642	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831651	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831662	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831664	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72831685	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72831688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72833410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833412	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833413	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833414	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833415	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72833428	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72833431	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72833432	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7586893	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7587316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7599551	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv874868	chr2:113021811-113076095	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7596661	RGPD8	cis	Nerve Tibial	GTEx
rs7596661	RGPD8	cis	Adipose Subcutaneous	GTEx
rs7596661	RGPD8	cis	Esophagus Mucosa	GTEx
rs7596661	ZC3H8	cis	Artery Tibial	GTEx
rs7596661	RGPD8	cis	Esophagus Muscularis	GTEx
rs7596661	RGPD8	cis	Muscle Skeletal	GTEx
rs7596661	RGPD8	cis	Artery Aorta	GTEx
rs7596661	RGPD8	cis	Whole Blood	GTEx
rs7596661	RGPD8	cis	Thyroid	GTEx
rs7596661	RGPD8	cis	Artery Tibial	GTEx
rs7596661	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs7596661	LOC653596	cis	multi-tissue	Pritchard
rs7596661	RGPD8	cis	lung	GTEx
rs7596661	RGPD8	cis	Heart Left Ventricle	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113017800-113026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:113025200-113032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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