Variant report

Variant	rs12242299
Chromosome Location	chr10:49953604-49953605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10508907	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10776642	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10857626	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10857632	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10857633	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11101442	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17836423	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs1871599	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1993986	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2377627	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2377628	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4838645	0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4838646	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs7076662	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7099117	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv947977	chr10:49951534-49953881	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49923400-49960200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr10:49928400-49953800	Strong transcription	Primary hematopoietic stem cells	blood
3	chr10:49931000-49956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr10:49934400-49955800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr10:49934600-49955800	Strong transcription	Primary B cells from cord blood	blood
6	chr10:49939600-49956200	Weak transcription	Adipose Nuclei	Adipose
7	chr10:49948600-49957200	Weak transcription	Esophagus	oesophagus
8	chr10:49952000-49953800	Weak transcription	Lung	lung
9	chr10:49952000-49955800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr10:49952000-49956400	Weak transcription	Spleen	Spleen
11	chr10:49952000-49960800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr10:49952800-49955200	Weak transcription	Colonic Mucosa	Colon
13	chr10:49953000-49954000	Strong transcription	GM12878-XiMat	blood
14	chr10:49953400-49953800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:49953400-49960200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:49953600-49954000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr10:49953600-49954000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:49953600-49954200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
19	chr10:49953600-49954200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:49953600-49954200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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