Variant report

Variant	rs1882620
Chromosome Location	chr5:112648310-112648311
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	chr5:112637840..112639791-chr5:112646688..112648404,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10037836	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10037845	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10038017	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10040533	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10040770	1.00[EUR][1000 genomes]
rs10043512	0.86[ASN][1000 genomes]
rs10044201	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10051109	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10056104	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10058535	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10059129	0.94[EUR][1000 genomes]
rs10070884	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10070990	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10074346	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10075447	0.94[EUR][1000 genomes]
rs10077020	1.00[CEU][hapmap]
rs10478121	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10519344	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11953478	0.94[EUR][1000 genomes]
rs11954016	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11954410	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11958613	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11958734	1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12108831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356396	0.81[EUR][1000 genomes]
rs13361059	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13361060	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13362158	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1443691	1.00[JPT][hapmap]
rs17135493	0.85[EUR][1000 genomes]
rs17135568	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17135570	0.86[ASN][1000 genomes]
rs2068922	1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28462299	0.86[ASN][1000 genomes]
rs28494592	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55794576	0.94[EUR][1000 genomes]
rs56875463	0.94[EUR][1000 genomes]
rs57727389	0.86[ASN][1000 genomes]
rs61560548	0.86[ASN][1000 genomes]
rs6868620	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6871995	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6874313	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6874561	0.85[EUR][1000 genomes]
rs73779001	1.00[EUR][1000 genomes]
rs73779022	0.94[EUR][1000 genomes]
rs73781511	1.00[ASN][1000 genomes]
rs73781512	0.86[ASN][1000 genomes]
rs73781513	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73781514	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7700940	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7707680	1.00[JPT][hapmap]
rs7718459	0.86[ASN][1000 genomes]
rs7719166	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7720189	0.86[ASN][1000 genomes]
rs7736171	0.86[ASN][1000 genomes]
rs9285877	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9326881	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9326882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9326883	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1018078	chr5:112615220-112657404	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv528805	chr5:112641650-112650751	Enhancers Genic enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112647200-112649000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:112647800-112648800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:112647800-112649200	Enhancers	HSMM	muscle
4	chr5:112648000-112648800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:112648000-112648800	Enhancers	A549	lung
6	chr5:112648000-112649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:112648000-112649200	Enhancers	Hela-S3	cervix
8	chr5:112648000-112649200	Enhancers	HMEC	breast
9	chr5:112648200-112648400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:112648200-112648800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr5:112648200-112648800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:112648200-112648800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:112648200-112648800	Enhancers	Osteobl	bone
14	chr5:112648200-112649000	Enhancers	NHEK	skin
15	chr5:112648200-112649200	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links