Variant report

Variant	rs606229
Chromosome Location	chr7:124772857-124772858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:124768386..124770245-chr7:124771796..124774751,2	MCF-7	breast:

Extended variants
information (count: 182 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs1006334	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs10081290	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1021080	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.84[ASN][1000 genomes]
rs10227119	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10228686	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10234592	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10239507	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10247349	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10252579	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10252798	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10254199	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10255638	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs10256218	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10257712	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs10258873	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10264210	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10264288	0.93[ASW][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap]
rs1026836	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs1026837	0.85[ASN][1000 genomes]
rs1026839	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10269342	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs10270051	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10274820	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10275346	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs10276834	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1031955	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs10500098	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10954056	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10954062	0.84[ASN][1000 genomes]
rs11761669	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs11763920	0.85[ASN][1000 genomes]
rs11767649	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11767737	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11975363	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11980178	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12112909	0.85[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.88[MKK][hapmap];0.87[YRI][hapmap]
rs12113765	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs12533918	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs12534466	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12535807	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs12537431	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12538641	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12539580	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs12540261	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs13224820	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs13231916	0.85[ASN][1000 genomes]
rs13233978	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs13234368	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs13234634	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs13240043	0.84[ASN][1000 genomes]
rs1351471	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1383749	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1383750	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs1404898	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1471571	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1481327	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1481328	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1481329	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1481330	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1481331	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1481332	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1481337	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs1481338	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1481339	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1481342	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1481343	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1525614	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs1525618	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1525619	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs1531715	0.84[ASN][1000 genomes]
rs1531716	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1552118	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1552119	0.84[ASN][1000 genomes]
rs1552120	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.85[ASN][1000 genomes]
rs1600738	0.85[ASN][1000 genomes]
rs1600739	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1600740	0.85[ASN][1000 genomes]
rs1600741	0.83[YRI][hapmap]
rs1871770	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1871771	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1986124	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1994022	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1994024	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap]
rs1994025	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2017928	0.84[ASN][1000 genomes]
rs2170351	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2219953	0.85[ASN][1000 genomes]
rs2402756	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2402757	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2402762	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2402763	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs28491035	0.82[ASN][1000 genomes]
rs2929320	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2929323	0.92[ASN][1000 genomes]
rs2949802	0.92[ASN][1000 genomes]
rs2968865	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap]
rs2968867	0.92[ASN][1000 genomes]
rs34630567	0.84[ASN][1000 genomes]
rs34865746	0.85[ASN][1000 genomes]
rs3900363	0.85[ASN][1000 genomes]
rs3903521	0.85[ASN][1000 genomes]
rs3903522	0.85[ASN][1000 genomes]
rs3903523	0.85[ASN][1000 genomes]
rs4272297	0.85[ASN][1000 genomes]
rs585608	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs589823	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597279	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs607260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616697	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs628365	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs632459	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]
rs635682	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs635736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636721	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637482	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639239	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466966	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6466968	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6466982	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6466989	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6466990	0.87[ASN][1000 genomes]
rs6466993	0.86[ASN][1000 genomes]
rs648619	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs651869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659987	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs662165	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs665753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672965	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676037	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683707	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs684345	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685909	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942997	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs6945951	0.85[ASN][1000 genomes]
rs6952915	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs6954614	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6957525	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6961441	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6963594	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6964090	0.85[ASN][1000 genomes]
rs6967707	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6971179	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6977313	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs719972	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.84[ASN][1000 genomes]
rs723444	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap]
rs7776821	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7778875	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7779594	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7780392	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7786384	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7787605	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs7788066	0.84[ASN][1000 genomes]
rs7788458	0.84[ASN][1000 genomes]
rs7791488	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7792654	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7794565	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7794959	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7795233	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7795605	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7795611	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7795934	0.84[ASN][1000 genomes]
rs7799518	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs7799535	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7799712	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7802007	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7802210	0.84[ASN][1000 genomes]
rs7806530	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs7806548	0.92[ASN][1000 genomes]
rs7810654	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs792627	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs900047	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs922711	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs922712	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs9691875	0.84[ASN][1000 genomes]
rs9692367	0.84[ASN][1000 genomes]
rs998054	0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs606229	RP11-3B12.1	cis	Artery Tibial	GTEx
rs606229	ASB15	cis	cerebellum	SCAN
rs606229	KCP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124739800-124776000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:124771000-124776400	Weak transcription	HUVEC	blood vessel

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