Variant report

Variant	rs10962520
Chromosome Location	chr9:16656687-16656688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1003069	0.81[YRI][hapmap]
rs1029015	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10756757	0.81[CEU][hapmap]
rs10756762	0.81[CEU][hapmap]
rs10756772	0.89[ASN][1000 genomes]
rs10756773	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs10810579	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs10810580	0.83[YRI][hapmap]
rs10810581	0.83[YRI][hapmap]
rs10962519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790341	0.82[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs13290470	0.84[CHB][hapmap]
rs1415471	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs1890074	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2050617	0.85[CHB][hapmap]
rs2275256	0.92[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4961727	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs4961728	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7019299	0.93[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs7023752	0.87[CEU][hapmap]
rs7033512	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7034582	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7043298	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7046245	0.88[EUR][1000 genomes]
rs943737	0.82[CEU][hapmap]
rs943738	0.82[CEU][hapmap]
rs9886876	0.86[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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv430000	chr9:16603483-16671045	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16640000-16670800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16646200-16656800	Weak transcription	HSMMtube	muscle
3	chr9:16646600-16661000	Weak transcription	HSMM	muscle
4	chr9:16650800-16657600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:16651200-16656800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr9:16651400-16656800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:16652400-16656800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:16653600-16657000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr9:16654200-16656800	Weak transcription	NH-A	brain
10	chr9:16654200-16660400	Weak transcription	Esophagus	oesophagus
11	chr9:16654400-16656800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr9:16654400-16657600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:16654400-16669200	Weak transcription	NHLF	lung
14	chr9:16654600-16657600	Enhancers	Colon Smooth Muscle	Colon
15	chr9:16654600-16657600	Enhancers	Osteobl	bone
16	chr9:16654800-16658200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:16655000-16658800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:16655000-16666600	Weak transcription	Fetal Stomach	stomach
19	chr9:16655600-16657200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr9:16655600-16657800	Enhancers	Stomach Smooth Muscle	stomach
21	chr9:16655600-16661400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:16655800-16657200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:16655800-16657600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:16655800-16657600	Enhancers	Adipose Nuclei	Adipose
25	chr9:16655800-16657600	Enhancers	Ovary	ovary
26	chr9:16655800-16657600	Enhancers	Psoas Muscle	Psoas
27	chr9:16656000-16656800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:16656000-16657200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:16656000-16657600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:16656000-16657600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:16656200-16658800	Weak transcription	Fetal Lung	lung
32	chr9:16656400-16658600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:16656400-16660200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:16656400-16660800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:16656400-16661200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:16656600-16657000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr9:16656600-16657600	Enhancers	Rectal Smooth Muscle	rectum
38	chr9:16656600-16670800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links