Variant report

Variant	rs7865971
Chromosome Location	chr9:117905403-117905404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:117905070-117905528	U87	brain:	n/a	n/a
2	POLR2A	chr9:117905113-117905528	U87	brain:	n/a	n/a
3	POLR2A	chr9:117904995-117905595	U87	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000236461	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1000109	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1000110	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1000111	0.96[CEU][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10759756	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10759757	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10817714	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10817715	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10817716	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10817718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10982550	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10982557	0.83[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982572	0.83[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10982576	0.88[ASN][1000 genomes]
rs10982598	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1111784	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11788578	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11792657	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11793679	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11794627	0.88[ASN][1000 genomes]
rs12376564	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12376870	0.94[ASN][1000 genomes]
rs12378459	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12379019	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12380363	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12554357	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12554651	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1335350	0.86[CHB][hapmap]
rs1360290	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1411458	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1414146	0.86[CHB][hapmap]
rs16936516	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2001693	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012566	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2012775	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2900594	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3748166	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4448357	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4587405	0.83[ASN][1000 genomes]
rs4978620	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4979499	0.83[CEU][hapmap]
rs4979500	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4979501	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4979503	0.96[CEU][hapmap]
rs4979506	0.83[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57814325	0.94[ASN][1000 genomes]
rs58134557	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58160054	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61508829	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62580502	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6478132	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7018653	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7021057	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7024048	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7025283	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029482	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7029844	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7035705	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7039636	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7039915	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7040243	0.86[CHB][hapmap]
rs7040521	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7849460	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7849467	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7850000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850007	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7851185	0.86[CHB][hapmap]
rs7858535	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs884790	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv6681	chr9:117893926-117938609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117890200-117909000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:117900000-117908400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:117904000-117907400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:117904200-117907000	Enhancers	Brain Hippocampus Middle	brain
5	chr9:117904200-117909200	Weak transcription	Aorta	Aorta
6	chr9:117904400-117906000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:117904600-117905600	Enhancers	Brain Cingulate Gyrus	brain
8	chr9:117904800-117905600	Enhancers	Rectal Smooth Muscle	rectum
9	chr9:117904800-117907600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:117904800-117910000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:117904800-117910200	Enhancers	NHDF-Ad	bronchial
12	chr9:117905000-117905600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:117905000-117906000	Enhancers	HSMM	muscle
14	chr9:117905000-117907800	Enhancers	Dnd41	blood
15	chr9:117905000-117910000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:117905000-117910200	Enhancers	Osteobl	bone
17	chr9:117905400-117907000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:117905400-117908000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:117905400-117908200	Weak transcription	NHLF	lung

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