Variant report

Variant	rs2040390
Chromosome Location	chr3:46376501-46376502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1034382	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1799865	0.83[ASN][1000 genomes]
rs2040389	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2097282	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2097283	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2097284	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2157058	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2187669	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2187670	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2213288	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373226	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092962	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092963	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3092964	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3138042	0.83[ASN][1000 genomes]
rs34997146	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35510257	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36048784	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36118141	0.83[EUR][1000 genomes]
rs3762823	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3918358	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3918359	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3918361	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41276529	0.83[EUR][1000 genomes]
rs41418050	0.81[EUR][1000 genomes]
rs41502550	0.81[EUR][1000 genomes]
rs4683194	0.83[EUR][1000 genomes]
rs4683199	0.84[EUR][1000 genomes]
rs4683211	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4683215	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4683218	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62244813	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6441950	0.83[EUR][1000 genomes]
rs6441958	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6441959	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6441960	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441968	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441972	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67450950	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6765031	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783993	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6785981	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6788849	0.82[EUR][1000 genomes]
rs6801761	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810232	0.83[EUR][1000 genomes]
rs71327045	0.81[EUR][1000 genomes]
rs7371987	0.83[EUR][1000 genomes]
rs7432080	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7612940	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs762789	0.83[ASN][1000 genomes]
rs7635588	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs768539	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9839623	0.83[EUR][1000 genomes]
rs9840204	0.83[EUR][1000 genomes]
rs9877860	0.83[EUR][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46375000-46376800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:46375600-46377600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:46375600-46377600	Enhancers	HMEC	breast
4	chr3:46375800-46377600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:46375800-46377600	Enhancers	Hela-S3	cervix
6	chr3:46375800-46378200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:46376000-46380000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:46376400-46376800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:46376400-46376800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:46376400-46377000	Flanking Active TSS	NHEK	skin
11	chr3:46376400-46377400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:46376400-46377400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:46376400-46377600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links