Variant report

Variant	rs9877813
Chromosome Location	chr3:119872586-119872587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119812554..119815643-chr3:119870791..119873292,3	MCF-7	breast:
2	chr3:119812502..119815806-chr3:119871102..119874015,4	MCF-7	breast:
3	chr3:119871941..119873702-chr3:119897791..119900404,2	MCF-7	breast:
4	chr3:119865823..119868383-chr3:119871262..119874013,2	MCF-7	breast:
5	chr3:119870692..119873578-chr3:119876530..119878351,2	MCF-7	breast:
6	chr3:119872156..119875063-chr3:119876468..119880752,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10049457	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10804550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934518	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934519	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11706916	0.80[AMR][1000 genomes]
rs11710115	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs11719262	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs11721221	0.81[JPT][hapmap]
rs11926867	0.87[JPT][hapmap]
rs12489527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12495656	0.81[AMR][1000 genomes]
rs13087908	0.86[JPT][hapmap]
rs13317104	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs1873070	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2014142	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2029609	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732363	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57664228	0.81[AMR][1000 genomes]
rs59328871	0.81[AMR][1000 genomes]
rs62264984	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6772067	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7635647	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8180068	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs902793	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs9835042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9844508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9878040	0.94[AMR][1000 genomes];0.81[EUR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119867200-119873400	Weak transcription	HSMMtube	muscle
2	chr3:119870200-119872800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:119870400-119873000	Enhancers	HMEC	breast
4	chr3:119870800-119872600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:119870800-119873200	Enhancers	Placenta	Placenta
6	chr3:119871200-119872800	Weak transcription	Fetal Intestine Small	intestine
7	chr3:119871400-119873000	Enhancers	HUVEC	blood vessel
8	chr3:119871600-119872600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:119871800-119872600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:119871800-119872800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:119871800-119872800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:119871800-119872800	Flanking Active TSS	Hela-S3	cervix
13	chr3:119871800-119872800	Flanking Active TSS	NHDF-Ad	bronchial
14	chr3:119871800-119873000	Enhancers	NHLF	lung
15	chr3:119872000-119872600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:119872000-119872800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:119872200-119872800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:119872200-119872800	Enhancers	NHEK	skin
19	chr3:119872200-119872800	Enhancers	Osteobl	bone
20	chr3:119872200-119873000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:119872200-119873200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:119872400-119872800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:119872400-119877800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:119872400-119878800	Weak transcription	Placenta Amnion	Placenta Amnion

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