Variant report

Variant	rs12277628
Chromosome Location	chr11:58736398-58736399
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr11:58736374-58736639	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr11:58736357-58736612	MCF10A-Er-Src	breast:	n/a	n/a
3	HA-E2F1	chr11:58735777-58736416	MCF-7	breast:	n/a	chr11:58736144-58736151 chr11:58736143-58736152 chr11:58736144-58736151 chr11:58736144-58736151

Variant related genes	Relation type
ENSG00000254877	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10792206	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10792207	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10792209	0.99[AFR][1000 genomes]
rs10896872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896873	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896874	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896877	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896878	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896879	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896880	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896882	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896883	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896884	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896885	0.96[AFR][1000 genomes]
rs10896886	0.86[AFR][1000 genomes]
rs11229687	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229688	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229689	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229692	0.82[ASN][1000 genomes]
rs11229693	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229694	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229695	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229701	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229704	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229705	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229708	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11229711	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229713	0.96[AFR][1000 genomes]
rs11229714	0.96[AFR][1000 genomes]
rs12222588	0.82[JPT][hapmap]
rs12222597	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12223443	0.82[ASN][1000 genomes]
rs12270298	0.85[EUR][1000 genomes]
rs12272494	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12278662	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12281983	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12292314	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1808064	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1815856	0.89[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1893627	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1893628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1893629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938791	0.99[AFR][1000 genomes]
rs1943264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2156344	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2156345	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2156349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3740950	0.84[ASN][1000 genomes]
rs4271397	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4573693	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4939243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56155456	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58848038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61889804	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61889805	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61892604	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7108461	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7118637	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7126489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7129011	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73483072	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7930111	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7939049	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs948819	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9787921	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv3444895	chr11:58614102-58779384	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv3393019	chr11:58679419-58880845	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv428258	chr11:58700092-58878839	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers 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 lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	nsv832169	chr11:58700097-58861680	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv430387	chr11:58719050-58778643	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv832171	chr11:58725930-58878839	Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv469559	chr11:58730785-58887639	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv482906	chr11:58730785-58887639	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv471671	chr11:58730786-58887639	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58726600-58740000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr11:58730200-58739400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:58732000-58740000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr11:58735400-58736400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr11:58735600-58736400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:58735600-58736400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr11:58735600-58736400	Active TSS	Fetal Brain Female	brain
8	chr11:58735800-58736400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr11:58735800-58736400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:58735800-58736400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:58735800-58736800	Enhancers	Liver	Liver
12	chr11:58736200-58736400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:58736200-58736400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:58736200-58736400	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:58736200-58736400	Active TSS	Brain Germinal Matrix	brain
16	chr11:58736200-58736400	Enhancers	Osteobl	bone
17	chr11:58736200-58736600	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links