Variant report

Variant	rs2035669
Chromosome Location	chr3:119915437-119915438
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	chr3:119905802..119907944-chr3:119913665..119916564,2	MCF-7	breast:
2	chr3:119864581..119866968-chr3:119914610..119916835,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1074053	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934511	0.93[JPT][hapmap]
rs11707699	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710115	0.92[CEU][hapmap]
rs11712811	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11719262	0.92[CEU][hapmap]
rs11721221	0.91[CEU][hapmap]
rs11926867	0.86[CEU][hapmap]
rs13075809	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13088757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090279	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1488763	0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs17811405	0.83[CEU][hapmap]
rs334548	0.83[CEU][hapmap];0.88[TSI][hapmap]
rs334550	0.83[CEU][hapmap];0.88[TSI][hapmap]
rs35605064	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71327212	0.85[ASN][1000 genomes]
rs71327213	0.83[ASN][1000 genomes]
rs787202	0.85[TSI][hapmap]
rs902793	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv1008362	chr3:119901774-119919670	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2035669	PDIA5	cis	cerebellum	SCAN
rs2035669	ARHGAP31	cis	parietal	SCAN
rs2035669	SEMA5B	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119896400-119921400	Weak transcription	Ovary	ovary
2	chr3:119897000-119921400	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:119900800-119915600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:119911800-119921400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:119912000-119917000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:119914400-119916000	Enhancers	NHEK	skin
7	chr3:119914600-119916000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:119914600-119916200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:119915000-119916600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:119915000-119917200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:119915200-119915600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:119915200-119915800	Enhancers	HMEC	breast
13	chr3:119915200-119916000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:119915400-119916200	Enhancers	HUES48 Cell Line	embryonic stem cell

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