Variant report

Variant	rs2365490
Chromosome Location	chr3:158952645-158952646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10470473	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10513537	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10936173	0.87[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs10936175	0.88[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs10936176	0.88[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11715082	0.88[CEU][hapmap]
rs11924990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13326945	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs1449021	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17727250	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1823311	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1868414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2122147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2365483	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs6441253	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs6777541	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6781221	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs6791853	0.87[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs720397	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs7630467	1.00[CHB][hapmap]
rs7639623	0.89[ASN][1000 genomes]
rs9283610	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs9820047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9821641	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs9823142	0.85[ASN][1000 genomes]
rs9827242	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9827400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9829189	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9831067	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs9834328	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs9838646	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs9839112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9840972	0.81[EUR][1000 genomes]
rs9852196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9856166	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs9862769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9878883	0.81[EUR][1000 genomes]
rs9880642	0.88[CEU][hapmap];0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3426016	chr3:158676623-158979242	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv491927	chr3:158692653-158952780	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158951800-158953000	Enhancers	Muscle Satellite Cultured Cells	--
2	chr3:158951800-158953200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:158952000-158952800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:158952000-158957400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:158952200-158952800	Enhancers	NHLF	lung
6	chr3:158952400-158952800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:158952400-158953000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:158952400-158954200	Weak transcription	Osteobl	bone

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