Variant report

Variant	rs7625177
Chromosome Location	chr3:135699877-135699878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135684450..135686631-chr3:135698740..135700367,2	MCF-7	breast:
2	chr3:135693339..135695483-chr3:135697510..135700287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073711	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs12630389	0.81[ASN][1000 genomes]
rs12632791	0.85[ASN][1000 genomes]
rs12633805	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12637541	0.83[ASN][1000 genomes]
rs13059064	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065499	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13069408	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13072433	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13072690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075579	0.87[ASN][1000 genomes]
rs13078865	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13079037	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13084404	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13092707	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13097172	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13097176	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13097267	0.88[ASN][1000 genomes]
rs13100235	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1523593	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1523598	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1523599	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1523600	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs16843560	0.82[ASN][1000 genomes]
rs16843611	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2140450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177407	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2400649	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34447526	0.88[ASN][1000 genomes]
rs35097316	0.83[ASN][1000 genomes]
rs35532770	0.87[ASN][1000 genomes]
rs35946332	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35961065	0.85[ASN][1000 genomes]
rs3946444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075999	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4331626	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678224	0.86[ASN][1000 genomes]
rs4678288	0.88[ASN][1000 genomes]
rs4678432	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4678434	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4678435	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs55873361	0.88[ASN][1000 genomes]
rs56152207	0.88[ASN][1000 genomes]
rs57594457	0.88[ASN][1000 genomes]
rs60070757	0.88[ASN][1000 genomes]
rs61791712	0.88[ASN][1000 genomes]
rs61791714	0.88[ASN][1000 genomes]
rs6439603	0.82[ASN][1000 genomes]
rs6439605	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439609	0.83[ASN][1000 genomes]
rs6439610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439614	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439615	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439618	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439622	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439623	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439624	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6770366	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771950	0.88[ASN][1000 genomes]
rs6775261	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779903	0.93[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs6793273	0.80[ASN][1000 genomes]
rs6803786	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7433592	0.88[ASN][1000 genomes]
rs7610302	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625607	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7635621	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650079	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9289501	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs940229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9758578	0.89[ASN][1000 genomes]
rs9846554	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9852009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856799	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs9868239	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	esv3463539	chr3:135696927-135701248	Weak transcription Flanking Active TSS Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3463540	chr3:135696927-135701248	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2421767	chr3:135697373-135699877	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7625177	PCCB	cis	cerebellum	SCAN
rs7625177	ZBTB38	cis	cerebellum	SCAN
rs7625177	PCCB	cis	lymphoblastoid	seeQTL
rs7625177	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135687600-135700400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:135690200-135701200	Weak transcription	NHEK	skin
3	chr3:135690200-135701400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:135690400-135700800	Weak transcription	HSMM	muscle
5	chr3:135693000-135700600	Weak transcription	Pancreas	Pancrea
6	chr3:135693000-135701400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:135693400-135700600	Weak transcription	NH-A	brain
8	chr3:135693400-135701400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:135693600-135701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:135693600-135704000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:135694000-135700800	Weak transcription	Aorta	Aorta
12	chr3:135694000-135713600	Weak transcription	Fetal Lung	lung
13	chr3:135694000-135726600	Weak transcription	Esophagus	oesophagus
14	chr3:135694200-135701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:135694200-135702000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:135694200-135707400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:135694200-135707400	Weak transcription	Gastric	stomach
18	chr3:135694200-135708800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:135694200-135709600	Weak transcription	Right Atrium	heart
20	chr3:135694200-135713400	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:135698400-135702600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr3:135698800-135700600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:135699000-135703200	Enhancers	Colon Smooth Muscle	Colon
24	chr3:135699000-135704800	Enhancers	Rectal Smooth Muscle	rectum
25	chr3:135699200-135700200	Weak transcription	Fetal Intestine Large	intestine
26	chr3:135699600-135700000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:135699600-135700200	Enhancers	Brain Substantia Nigra	brain
28	chr3:135699600-135700400	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr3:135699600-135701000	Enhancers	Ovary	ovary
30	chr3:135699600-135702000	Enhancers	Psoas Muscle	Psoas
31	chr3:135699600-135702000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:135699600-135702600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:135699600-135703400	Enhancers	NHDF-Ad	bronchial
34	chr3:135699800-135701400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:135699800-135702200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:135699800-135703200	Enhancers	NHLF	lung
37	chr3:135699800-135709600	Weak transcription	Right Ventricle	heart

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