Variant report

Variant	rs62575309
Chromosome Location	chr9:118377251-118377252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12000608	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12002475	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12003493	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2188068	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575261	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575263	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62575313	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62576528	1.00[AFR][1000 genomes]
rs62576529	1.00[AFR][1000 genomes]
rs62576536	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62576537	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62576538	0.82[AMR][1000 genomes]
rs62576539	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62576662	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62576663	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62576664	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62576666	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62576667	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62576696	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62576698	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576702	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755374	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72757379	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72759322	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72763123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1046948	chr9:118185587-118926891	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv916622	chr9:118206309-118952390	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv540207	chr9:118206311-118920304	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv491661	chr9:118206312-118802177	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv831698	chr9:118284259-118446456	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1047164	chr9:118286742-118456851	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62575309	RP11-445L6.3	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118358400-118377800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:118372800-118377400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:118376600-118377400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:118376600-118377600	Enhancers	Osteobl	bone
5	chr9:118376600-118377800	Enhancers	NHEK	skin
6	chr9:118376600-118377800	Enhancers	NHLF	lung
7	chr9:118376600-118378200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:118376600-118379000	Enhancers	HSMM	muscle
9	chr9:118376600-118379800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:118376600-118379800	Enhancers	NHDF-Ad	bronchial
11	chr9:118376600-118380000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:118376600-118380000	Enhancers	HMEC	breast
13	chr9:118376800-118377400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:118376800-118377400	Enhancers	A549	lung
15	chr9:118376800-118377400	Enhancers	Hela-S3	cervix
16	chr9:118376800-118377800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:118376800-118379000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:118376800-118379400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:118376800-118379800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:118377000-118377800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:118377000-118379600	Enhancers	Placenta Amnion	Placenta Amnion
22	chr9:118377200-118377400	Flanking Active TSS	NH-A	brain
23	chr9:118377200-118378200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:118377200-118378200	Flanking Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links