Variant report

Variant	rs2054162
Chromosome Location	chr2:173533225-173533226
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12615889	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622335	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12622834	0.84[ASN][1000 genomes]
rs16860778	0.85[ASN][1000 genomes]
rs16860794	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860795	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860796	0.84[ASN][1000 genomes]
rs16860798	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860805	0.88[EUR][1000 genomes]
rs16860809	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2034854	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2054163	0.87[ASN][1000 genomes]
rs2084731	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084732	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2122832	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2198799	0.85[ASN][1000 genomes]
rs2198800	0.85[ASN][1000 genomes]
rs4313941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4404239	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4482449	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4972514	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4972515	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4972516	0.81[ASN][1000 genomes]
rs4972845	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4972847	0.85[ASN][1000 genomes]
rs4972848	0.85[ASN][1000 genomes]
rs4972849	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4972850	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4972851	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4972852	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56750684	0.80[ASN][1000 genomes]
rs57566649	0.83[ASN][1000 genomes]
rs58308687	0.85[ASN][1000 genomes]
rs59103702	0.84[ASN][1000 genomes]
rs59547791	0.85[ASN][1000 genomes]
rs59839960	0.85[ASN][1000 genomes]
rs61556691	0.81[ASN][1000 genomes]
rs6705827	0.84[ASN][1000 genomes]
rs6716527	0.85[ASN][1000 genomes]
rs73042937	0.85[ASN][1000 genomes]
rs733331	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7590282	0.85[ASN][1000 genomes]
rs7595971	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173521400-173536800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:173530400-173536400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:173530600-173536400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:173530800-173536400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:173531800-173533400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:173532000-173533400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:173532000-173533400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:173532000-173533400	Enhancers	NHDF-Ad	bronchial
9	chr2:173532200-173533400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:173532200-173533400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:173532200-173533400	Enhancers	NHLF	lung
12	chr2:173532400-173536400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:173532800-173533400	Enhancers	Osteobl	bone
14	chr2:173533000-173536800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:173533200-173535000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:173533200-173536400	Weak transcription	Muscle Satellite Cultured Cells	--

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