Variant report

Variant	rs339664
Chromosome Location	chr3:42808493-42808494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10865923	0.99[ASN][1000 genomes]
rs11129969	0.90[JPT][hapmap]
rs11709500	0.90[JPT][hapmap]
rs11710120	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11713172	0.90[JPT][hapmap]
rs11717346	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11915803	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17238798	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2240861	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs339667	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339668	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339676	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339681	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs4682856	0.91[JPT][hapmap]
rs4682857	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4683336	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs55641040	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58045017	0.82[ASN][1000 genomes]
rs62246636	0.82[ASN][1000 genomes]
rs6442057	0.88[JPT][hapmap]
rs6764909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7634876	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9880635	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 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	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42793600-42811000	Weak transcription	Lung	lung
3	chr3:42795600-42814000	Weak transcription	Gastric	stomach
4	chr3:42795600-42814400	Weak transcription	Aorta	Aorta
5	chr3:42800400-42808600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:42803000-42814200	Weak transcription	Right Atrium	heart
7	chr3:42804200-42814200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:42805000-42813800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:42806200-42809800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:42807400-42813400	Weak transcription	Primary B cells from cord blood	blood
11	chr3:42807400-42814000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:42807800-42811000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:42808000-42812400	Weak transcription	HepG2	liver
14	chr3:42808000-42814000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:42808000-42814200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:42808400-42808800	Enhancers	Monocytes-CD14+_RO01746	blood

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