Variant report

Variant	rs2647496
Chromosome Location	chr1:77958105-77958106
allele	C/T
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:33)

rs_ID	r²[population]
rs11800652	0.92[JPT][hapmap]
rs11810135	0.91[JPT][hapmap]
rs12564592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12564604	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12568374	0.92[JPT][hapmap]
rs12568376	0.91[JPT][hapmap]
rs12731121	0.80[AMR][1000 genomes]
rs13376422	0.84[EUR][1000 genomes]
rs17380852	0.93[CEU][hapmap]
rs2245189	0.87[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2454328	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2647497	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35254623	0.82[AMR][1000 genomes]
rs35635429	0.80[AMR][1000 genomes]
rs35883964	0.82[AMR][1000 genomes]
rs4949655	0.91[JPT][hapmap]
rs4949803	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs58143971	0.98[ASN][1000 genomes]
rs58397190	0.93[ASN][1000 genomes]
rs58958142	0.97[ASN][1000 genomes]
rs59076612	0.80[ASN][1000 genomes]
rs59623467	0.97[ASN][1000 genomes]
rs60207382	0.97[ASN][1000 genomes]
rs66538606	0.80[AMR][1000 genomes]
rs6664497	0.83[ASN][1000 genomes]
rs6680677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs74090603	0.82[ASN][1000 genomes]
rs74090608	0.97[ASN][1000 genomes]
rs74090614	0.97[ASN][1000 genomes]
rs74090617	0.98[ASN][1000 genomes]
rs74090618	0.98[ASN][1000 genomes]
rs74090619	0.98[ASN][1000 genomes]
rs74092662	0.80[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	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77913200-77968400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:77940600-77960800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:77945400-77958600	Weak transcription	Primary T cells from cord blood	blood
4	chr1:77945800-77961600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:77954800-77958600	Enhancers	Brain Substantia Nigra	brain
6	chr1:77955400-77958200	Enhancers	Fetal Brain Male	brain
7	chr1:77955800-77964400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:77956000-77960800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:77956000-77961600	Weak transcription	NHLF	lung
10	chr1:77956000-77964600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:77956200-77958400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:77956200-77958600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr1:77956200-77959000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:77956200-77959400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:77956200-77961600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:77956200-77964000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:77956200-77964200	Weak transcription	NHDF-Ad	bronchial
18	chr1:77956200-77964400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:77956200-77975600	Weak transcription	HSMMtube	muscle
20	chr1:77956600-77958200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:77957400-77958200	Enhancers	Brain Angular Gyrus	brain
22	chr1:77957800-77958400	Enhancers	Brain Hippocampus Middle	brain
23	chr1:77958000-77958200	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:77958000-77958600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:77958000-77958800	Enhancers	Brain Anterior Caudate	brain
26	chr1:77958000-77960000	Strong transcription	HSMM	muscle

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