Variant report

Variant	rs7428398
Chromosome Location	chr3:139218529-139218530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10513063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1602626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1602628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17335312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17395611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17494356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs17494482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17560106	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs184156	1.00[JPT][hapmap]
rs184157	0.82[JPT][hapmap]
rs2289348	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2289350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2291555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2307031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2882080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295490	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs3772871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs397940	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs41356949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41399544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55922868	0.80[ASN][1000 genomes]
rs57707457	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57995350	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59628512	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61034702	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61680644	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9821204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9837167	0.95[ASN][1000 genomes]
rs9862672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1001460	chr3:139194633-139241616	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139208200-139249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:139213200-139228400	Weak transcription	Gastric	stomach
3	chr3:139213400-139234200	Weak transcription	Ovary	ovary
4	chr3:139213400-139235600	Weak transcription	Pancreas	Pancrea
5	chr3:139213400-139235600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:139213400-139239000	Weak transcription	Brain Substantia Nigra	brain
7	chr3:139213600-139234800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:139217400-139236000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:139218400-139218800	Enhancers	Fetal Intestine Large	intestine
10	chr3:139218400-139219000	Enhancers	Fetal Intestine Small	intestine

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