Variant report

Variant	rs632459
Chromosome Location	chr7:124788642-124788643
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	chr7:124783039..124785786-chr7:124787614..124790434,2	MCF-7	breast:

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1006334	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs1021080	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10227119	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs10228686	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10234592	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs10239507	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10247349	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10252579	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs10252798	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10254199	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10256218	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10257712	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10258873	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10264210	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1026836	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs1026839	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs10269342	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs10270051	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10274820	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10275346	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs10276834	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1031955	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10500098	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10954056	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs11767649	0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs11767737	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs11975363	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs11980178	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs12113765	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12533918	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs12534466	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs12535807	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs12538641	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs12539580	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs13224820	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs13234368	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs13234634	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1383749	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs1383750	0.95[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs1404898	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1471571	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1481327	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs1481328	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs1481329	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1481330	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1481337	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs1481338	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs1481342	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1481343	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1525614	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs1525618	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1525619	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1531716	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1552118	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1552120	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1600739	0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs1728929	0.85[EUR][1000 genomes]
rs1728930	0.85[EUR][1000 genomes]
rs1871770	0.95[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs1871771	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1986124	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1994024	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1994025	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2170351	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2402757	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs2402762	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs2402763	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2968865	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs585608	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs589823	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs597279	0.83[ASN][1000 genomes]
rs606229	0.86[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.87[ASN][1000 genomes]
rs607260	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs616697	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs628365	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap]
rs635682	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs635736	0.87[ASN][1000 genomes]
rs636161	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs636721	0.87[ASN][1000 genomes]
rs637482	0.83[ASN][1000 genomes]
rs639239	0.87[ASN][1000 genomes]
rs6466982	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs6466989	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs648619	0.87[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap]
rs651869	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs659987	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs662165	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs665753	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.87[ASN][1000 genomes]
rs672965	0.83[ASN][1000 genomes]
rs676037	0.86[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.83[ASN][1000 genomes]
rs683707	0.86[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.83[ASN][1000 genomes]
rs684345	0.86[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.87[ASN][1000 genomes]
rs685909	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs6942997	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs6952915	0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs6954614	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs6957525	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs6961441	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs6963594	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs6967707	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs6971179	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs6977313	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs719972	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs723444	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7776821	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs7778875	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs7779594	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7787605	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs7792654	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7794565	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7794959	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7799535	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7799712	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs7802007	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs7806530	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs7810654	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs792627	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs900047	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs922711	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs922712	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs998054	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	esv3394090	chr7:124602150-124900799	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv464708	chr7:124703756-124805279	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv608344	chr7:124703756-124805279	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv831119	chr7:124714009-124890119	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv2422188	chr7:124782873-125254203	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs632459	RP11-3B12.1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124785600-124789200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:124787200-124789200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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