Variant report

Variant	rs7635647
Chromosome Location	chr3:119896657-119896658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119896267..119897823-chr3:119902121..119903746,2	MCF-7	breast:
2	chr3:119810057..119817149-chr3:119894256..119903865,22	MCF-7	breast:
3	chr3:119809943..119817218-chr3:119893934..119905581,30	MCF-7	breast:
4	chr3:119887283..119893170-chr3:119894592..119900399,7	MCF-7	breast:
5	chr3:119877444..119878944-chr3:119896183..119899107,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10049457	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10804550	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10934519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11710115	0.90[JPT][hapmap]
rs11719262	0.85[JPT][hapmap]
rs11721221	0.90[JPT][hapmap]
rs11926867	1.00[JPT][hapmap]
rs12489527	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13087908	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs13317104	0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1388754	0.91[CHD][hapmap];0.83[GIH][hapmap]
rs1873070	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2014142	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029609	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732363	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62264984	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6772067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180068	0.88[CEU][hapmap]
rs902793	0.90[JPT][hapmap]
rs9835042	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844508	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9861883	0.86[TSI][hapmap]
rs9877813	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]
rs9878040	0.97[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
8	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
9	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
10	nsv518052	chr3:119893257-119896657	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7635647	PDIA5	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119892400-119914200	Weak transcription	Fetal Brain Female	brain
2	chr3:119893600-119897400	Enhancers	Placenta	Placenta
3	chr3:119895200-119897200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:119895400-119897000	Enhancers	Psoas Muscle	Psoas
5	chr3:119895400-119897200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:119895600-119896800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:119895600-119897000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr3:119895600-119897000	Enhancers	Fetal Muscle Leg	muscle
9	chr3:119895600-119897000	Enhancers	Right Ventricle	heart
10	chr3:119895600-119897000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:119895600-119897000	Flanking Active TSS	A549	lung
12	chr3:119895600-119897000	Flanking Active TSS	Hela-S3	cervix
13	chr3:119895600-119897200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:119895800-119896800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr3:119895800-119896800	Enhancers	Brain Anterior Caudate	brain
16	chr3:119895800-119896800	Enhancers	Fetal Intestine Large	intestine
17	chr3:119895800-119897000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:119895800-119897000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:119895800-119897000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:119895800-119897000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:119895800-119897000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:119895800-119897000	Enhancers	Colon Smooth Muscle	Colon
23	chr3:119895800-119897000	Enhancers	Fetal Lung	lung
24	chr3:119895800-119897000	Enhancers	Rectal Smooth Muscle	rectum
25	chr3:119895800-119897000	Enhancers	HSMM	muscle
26	chr3:119896000-119896800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:119896000-119897000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:119896000-119897000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:119896000-119897000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr3:119896000-119897000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr3:119896000-119897000	Enhancers	Fetal Stomach	stomach
32	chr3:119896000-119897000	Enhancers	Right Atrium	heart
33	chr3:119896000-119897000	Flanking Active TSS	Osteobl	bone
34	chr3:119896200-119896800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:119896200-119896800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr3:119896200-119896800	Flanking Active TSS	HMEC	breast
37	chr3:119896200-119896800	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:119896200-119897000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:119896200-119897000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:119896200-119897000	Enhancers	Aorta	Aorta
41	chr3:119896200-119897000	Flanking Active TSS	NHDF-Ad	bronchial
42	chr3:119896200-119897000	Flanking Active TSS	NHLF	lung
43	chr3:119896200-119897200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr3:119896200-119900000	Weak transcription	Fetal Intestine Small	intestine
45	chr3:119896400-119896800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:119896400-119896800	Enhancers	NH-A	brain
47	chr3:119896400-119897000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr3:119896400-119897000	Enhancers	Adipose Nuclei	Adipose
49	chr3:119896400-119897000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:119896400-119897000	Enhancers	HepG2	liver

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