Variant report

Variant	rs10962494
Chromosome Location	chr9:16574838-16574839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10116857	0.82[CEU][hapmap]
rs10117448	0.82[CEU][hapmap]
rs10123480	0.82[CEU][hapmap]
rs10123558	1.00[CEU][hapmap]
rs10511622	0.82[CEU][hapmap]
rs10733312	0.82[CEU][hapmap]
rs10738439	0.87[LWK][hapmap]
rs10756760	0.94[CHB][hapmap]
rs10756763	0.82[CEU][hapmap]
rs10810576	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810577	0.82[CHB][hapmap]
rs10962477	0.94[CHB][hapmap]
rs10962491	0.83[CHB][hapmap]
rs10962493	0.82[CEU][hapmap]
rs10962495	0.83[ASN][1000 genomes]
rs10962496	0.88[CHB][hapmap]
rs10962504	0.88[CHB][hapmap]
rs10962511	0.82[CEU][hapmap]
rs12002673	0.82[CEU][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.86[AFR][1000 genomes]
rs12338548	0.82[CEU][hapmap];0.80[MKK][hapmap]
rs12350242	0.82[CEU][hapmap]
rs12352543	0.82[CEU][hapmap]
rs1337393	0.82[CEU][hapmap]
rs1337400	0.82[CEU][hapmap]
rs1415474	0.82[CEU][hapmap]
rs1415476	0.82[CEU][hapmap]
rs1927616	0.82[CEU][hapmap]
rs1927617	0.82[CEU][hapmap]
rs1927618	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1927626	0.82[CEU][hapmap]
rs1952345	0.82[CEU][hapmap];0.88[AFR][1000 genomes]
rs1952346	0.82[CEU][hapmap]
rs2382808	0.82[CEU][hapmap]
rs2382809	0.82[CEU][hapmap]
rs2382810	0.82[CEU][hapmap]
rs2891072	0.82[CEU][hapmap]
rs4961723	0.94[CHB][hapmap]
rs6475059	0.82[CEU][hapmap]
rs6475060	0.82[CEU][hapmap]
rs6475062	0.82[CEU][hapmap]
rs725011	0.82[CEU][hapmap]
rs7350234	0.82[CEU][hapmap]
rs7470623	0.82[CEU][hapmap]
rs7850123	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs7856477	0.82[CEU][hapmap];0.84[LWK][hapmap]
rs7863885	0.86[YRI][hapmap]
rs7870380	0.82[CEU][hapmap]
rs943745	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv528443	chr9:16570142-16581967	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16553000-16575200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:16556400-16575600	Weak transcription	HSMM	muscle
3	chr9:16568800-16575200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:16569800-16582400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:16570800-16575800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr9:16571200-16575200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:16571400-16582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:16571800-16575600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:16572000-16575400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:16572000-16581800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:16572200-16575000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:16572400-16575000	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:16572400-16575600	Weak transcription	Adipose Nuclei	Adipose
14	chr9:16572600-16575400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:16572600-16575400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:16572600-16575600	Weak transcription	Osteobl	bone
17	chr9:16572800-16575200	Weak transcription	Fetal Kidney	kidney
18	chr9:16572800-16575200	Weak transcription	A549	lung
19	chr9:16572800-16575200	Weak transcription	NHLF	lung
20	chr9:16572800-16575400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:16572800-16575600	Weak transcription	Fetal Lung	lung
22	chr9:16572800-16575800	Weak transcription	NHDF-Ad	bronchial
23	chr9:16572800-16581400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:16572800-16581800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:16572800-16582600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:16573000-16575000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr9:16573000-16575000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:16573000-16575000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:16573000-16575400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:16573000-16575600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:16573000-16575600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:16573000-16575800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:16573200-16575200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:16573200-16575400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:16573200-16575600	Weak transcription	Colonic Mucosa	Colon
36	chr9:16573200-16586400	Weak transcription	Pancreas	Pancrea
37	chr9:16573200-16591800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr9:16574200-16575200	Weak transcription	Ovary	ovary
39	chr9:16574600-16580000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr9:16574800-16575200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:16574800-16575600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:16574800-16575600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr9:16574800-16576400	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr9:16574800-16576400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr9:16574800-16576600	Enhancers	Fetal Stomach	stomach

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