Variant report

Variant	rs390008
Chromosome Location	chr2:39163209-39163210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10173240	0.86[JPT][hapmap]
rs10204999	0.92[ASN][1000 genomes]
rs10779923	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11124654	0.80[ASN][1000 genomes]
rs11124655	0.85[ASN][1000 genomes]
rs11689954	0.81[JPT][hapmap]
rs12373604	0.82[AMR][1000 genomes]
rs12621073	0.81[ASN][1000 genomes]
rs12623330	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs12712621	0.93[JPT][hapmap]
rs12712625	0.81[CEU][hapmap];0.80[JPT][hapmap];0.87[YRI][hapmap]
rs12712627	0.81[CEU][hapmap];0.80[JPT][hapmap];0.87[YRI][hapmap]
rs13029388	0.82[CEU][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs13029406	0.86[JPT][hapmap]
rs13383541	0.87[JPT][hapmap]
rs1530852	0.86[JPT][hapmap]
rs1530853	0.86[JPT][hapmap]
rs1868867	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1901289	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1979142	0.86[JPT][hapmap]
rs373300	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[ASN][1000 genomes]
rs3770681	0.86[JPT][hapmap]
rs389023	0.95[ASN][1000 genomes]
rs4265996	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4641916	0.82[AMR][1000 genomes]
rs4670267	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6544180	0.81[ASN][1000 genomes]
rs6706091	0.87[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs6706186	0.92[ASN][1000 genomes]
rs6738403	0.81[AMR][1000 genomes]
rs6744514	0.86[YRI][hapmap]
rs7419616	0.86[JPT][hapmap]
rs7565111	0.87[JPT][hapmap]
rs7586929	0.86[AMR][1000 genomes]
rs7589162	0.87[JPT][hapmap];0.80[YRI][hapmap]
rs7598922	0.85[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes]
rs9808136	0.84[YRI][hapmap]
rs986019	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39110200-39186800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:39143800-39164600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:39145800-39172800	Weak transcription	Lung	lung
4	chr2:39147000-39166600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:39149000-39164800	Weak transcription	Ovary	ovary
6	chr2:39150000-39186600	Weak transcription	Brain Anterior Caudate	brain
7	chr2:39150400-39184800	Weak transcription	Psoas Muscle	Psoas
8	chr2:39155800-39174800	Weak transcription	Fetal Lung	lung
9	chr2:39156800-39172800	Weak transcription	Adipose Nuclei	Adipose
10	chr2:39160400-39164600	Weak transcription	HepG2	liver
11	chr2:39160400-39186600	Weak transcription	Pancreas	Pancrea
12	chr2:39161200-39164800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:39161400-39172400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:39162200-39163800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:39162400-39163400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:39162800-39163400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:39162800-39163600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:39163000-39163600	Enhancers	NHEK	skin
19	chr2:39163200-39163400	Enhancers	Osteobl	bone
20	chr2:39163200-39164400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:39163200-39174000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:39163200-39176000	Weak transcription	Brain Inferior Temporal Lobe	brain

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