Variant report

Variant	rs9872625
Chromosome Location	chr3:115880682-115880683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10934319	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11714784	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494524	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12632889	0.81[EUR][1000 genomes]
rs12634908	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12695322	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12695323	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs13062139	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13085102	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1381065	0.87[CEU][hapmap]
rs1381067	0.84[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap]
rs1461135	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1461136	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1461137	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1563933	0.84[CEU][hapmap]
rs17699134	0.82[CEU][hapmap]
rs1882012	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1903436	0.81[ASN][1000 genomes]
rs1920366	0.83[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1920374	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920376	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1950085	0.81[CEU][hapmap]
rs2126145	0.81[ASN][1000 genomes]
rs2169306	0.81[EUR][1000 genomes]
rs28673788	0.84[EUR][1000 genomes]
rs2902657	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4146785	0.90[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4296590	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4831124	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs5016488	0.81[ASN][1000 genomes]
rs6764630	0.95[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6784349	0.84[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs6792741	0.84[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs6795256	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs6795734	0.81[ASN][1000 genomes]
rs7629452	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7639609	0.82[CEU][hapmap]
rs7641216	0.83[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7641464	0.84[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7651629	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289046	0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9289047	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap]
rs9816326	0.81[ASN][1000 genomes]
rs9827410	0.84[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9851336	0.84[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap]
rs9864778	0.81[ASN][1000 genomes]
rs9875465	0.93[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9875621	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9875743	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9878125	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2751975	chr3:115766285-115902901	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2755046	chr3:115818840-115942952	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv591345	chr3:115819376-115902901	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2752728	chr3:115833212-115902901	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2751976	chr3:115867310-115903310	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115879600-115881000	Enhancers	Fetal Lung	lung
2	chr3:115880000-115881600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:115880000-115881600	Enhancers	Fetal Brain Male	brain
4	chr3:115880200-115880800	Flanking Active TSS	Brain Anterior Caudate	brain
5	chr3:115880200-115881000	Enhancers	Fetal Brain Female	brain
6	chr3:115880200-115881200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:115880400-115881000	Flanking Active TSS	Brain Angular Gyrus	brain
8	chr3:115880400-115881200	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr3:115880400-115881200	Flanking Active TSS	Brain Substantia Nigra	brain
10	chr3:115880400-115882000	Enhancers	Brain Germinal Matrix	brain
11	chr3:115880400-115884000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:115880600-115881000	Active TSS	Brain Cingulate Gyrus	brain
13	chr3:115880600-115881000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr3:115880600-115881000	Enhancers	Colon Smooth Muscle	Colon

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