Variant report

Variant	rs11712811
Chromosome Location	chr3:119877871-119877872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119872156..119875063-chr3:119876468..119880752,4	MCF-7	breast:
2	chr3:119811552..119816110-chr3:119876873..119880386,8	MCF-7	breast:
3	chr15:96452853..96454380-chr3:119876563..119879196,2	MCF-7	breast:
4	chr3:119865137..119868181-chr3:119877404..119880372,3	MCF-7	breast:
5	chr3:119870692..119873578-chr3:119876530..119878351,2	MCF-7	breast:
6	chr3:119877444..119878944-chr3:119896183..119899107,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1074053	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10934511	0.93[JPT][hapmap]
rs11707699	0.83[ASN][1000 genomes]
rs13075809	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13088757	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13090279	0.85[ASN][1000 genomes]
rs13092071	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1488763	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2035669	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs334548	0.81[TSI][hapmap]
rs334550	0.81[TSI][hapmap]
rs34591954	0.84[ASN][1000 genomes]
rs35605064	0.81[ASN][1000 genomes]
rs71327212	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71327213	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11712811	PDIA5	cis	cerebellum	SCAN
rs11712811	ARHGAP31	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119872400-119878800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119875200-119896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:119876000-119881400	Enhancers	Placenta	Placenta
4	chr3:119876400-119878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:119876400-119878800	Weak transcription	A549	lung
6	chr3:119876800-119878000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:119877000-119878800	Enhancers	Hela-S3	cervix
8	chr3:119877200-119879600	Enhancers	Fetal Intestine Small	intestine
9	chr3:119877400-119878400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:119877400-119878800	Weak transcription	Fetal Intestine Large	intestine
11	chr3:119877400-119879200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:119877600-119880000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:119877600-119881600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:119877600-119881600	Enhancers	HMEC	breast
15	chr3:119877600-119881600	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr3:119877600-119882600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr3:119877800-119878400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:119877800-119879400	Enhancers	Colon Smooth Muscle	Colon
19	chr3:119877800-119879600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:119877800-119879800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:119877800-119880400	Enhancers	NHEK	skin
22	chr3:119877800-119881600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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