Variant report

Variant	rs13299801
Chromosome Location	chr9:12878907-12878908
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12344174	0.93[EUR][1000 genomes]
rs13284880	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13286083	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13295684	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13297021	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13300480	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13301620	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1412308	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16929764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16929768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16929788	0.93[EUR][1000 genomes]
rs1831561	0.93[EUR][1000 genomes]
rs34040994	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34086294	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34297034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34660175	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35253144	0.82[EUR][1000 genomes]
rs35313919	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35685701	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35696782	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35858006	0.93[EUR][1000 genomes]
rs36050768	0.80[EUR][1000 genomes]
rs36080084	0.93[EUR][1000 genomes]
rs36196009	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71507337	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71507342	0.93[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	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv613615	chr9:12830070-12947238	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12875200-12884800	Weak transcription	HMEC	breast
2	chr9:12875600-12880000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:12875600-12880200	Weak transcription	NHDF-Ad	bronchial
4	chr9:12875800-12880600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:12876000-12880400	Weak transcription	NHEK	skin
6	chr9:12876800-12881600	Enhancers	Hela-S3	cervix
7	chr9:12877200-12879200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr9:12877200-12879800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr9:12877400-12879400	Enhancers	Fetal Intestine Small	intestine
10	chr9:12877400-12880400	Weak transcription	Fetal Kidney	kidney
11	chr9:12877400-12882000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:12877600-12882200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:12878000-12879200	Enhancers	Osteobl	bone
14	chr9:12878000-12880600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:12878000-12883000	Enhancers	A549	lung
16	chr9:12878200-12879000	Enhancers	Liver	Liver
17	chr9:12878200-12879000	Enhancers	HepG2	liver
18	chr9:12878200-12879200	Enhancers	HUVEC	blood vessel
19	chr9:12878400-12879000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:12878400-12879200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:12878400-12880400	Weak transcription	Fetal Intestine Large	intestine
22	chr9:12878400-12880600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:12878600-12879000	Enhancers	Fetal Lung	lung
24	chr9:12878600-12880400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links