Variant report

Variant	rs6475538
Chromosome Location	chr9:21542726-21542727
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10120766	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10124767	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10491566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10965048	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1332181	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1591035	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2025327	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2025328	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2039378	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2039379	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2146797	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183904	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2210437	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs720975	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs725074	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7863623	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7868724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][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	nsv892740	chr9:21471499-21551513	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
2	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
4	nsv892741	chr9:21517302-21551513	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21507200-21551400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:21529000-21551400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:21532200-21542800	Weak transcription	NHLF	lung
4	chr9:21534000-21543000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:21534000-21544200	Weak transcription	NHDF-Ad	bronchial
6	chr9:21534400-21548200	Weak transcription	HSMM	muscle
7	chr9:21536000-21543000	Weak transcription	NH-A	brain
8	chr9:21536400-21544400	Weak transcription	Hela-S3	cervix
9	chr9:21536400-21546800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:21536400-21552200	Weak transcription	Gastric	stomach
11	chr9:21536600-21548400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:21536600-21549600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:21536800-21542800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:21542000-21542800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:21542000-21543400	Genic enhancers	NHEK	skin
16	chr9:21542000-21543600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr9:21542000-21543600	Genic enhancers	Osteobl	bone
18	chr9:21542000-21544200	Genic enhancers	HMEC	breast
19	chr9:21542000-21545400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:21542200-21542800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:21542200-21542800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:21542200-21542800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr9:21542200-21542800	Weak transcription	Fetal Intestine Large	intestine
24	chr9:21542200-21543000	Weak transcription	Fetal Intestine Small	intestine
25	chr9:21542200-21551800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:21542600-21542800	Genic enhancers	A549	lung
27	chr9:21542600-21542800	Enhancers	HUVEC	blood vessel
28	chr9:21542600-21543000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:21542600-21543000	Enhancers	Duodenum Mucosa	Duodenum
30	chr9:21542600-21543200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:21542600-21543200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:21542600-21543200	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links