Variant report

Variant	rs339663
Chromosome Location	chr3:42809715-42809716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11129971	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11129973	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11708224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11720829	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12488173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13062528	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs1564176	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1564177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1991438	0.81[AFR][1000 genomes]
rs339669	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339673	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339675	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339679	0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35033264	1.00[MEX][hapmap]
rs35426298	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4399859	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4404423	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682855	0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683331	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683334	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs5027058	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60959614	0.85[AMR][1000 genomes]
rs6442065	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773636	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773675	1.00[MEX][hapmap]
rs6777653	1.00[MEX][hapmap]
rs6778695	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787667	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6802779	1.00[MEX][hapmap]
rs7610350	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7611520	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612614	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612782	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614158	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620291	0.88[AFR][1000 genomes]
rs7648688	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9755640	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9862147	0.85[AMR][1000 genomes]
rs9866005	0.81[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882356	1.00[MEX][hapmap];0.85[AMR][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:15 , 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	chr3:42803000-42814200	Weak transcription	Right Atrium	heart
6	chr3:42804200-42814200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:42805000-42813800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:42806200-42809800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:42807400-42813400	Weak transcription	Primary B cells from cord blood	blood
10	chr3:42807400-42814000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:42807800-42811000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:42808000-42812400	Weak transcription	HepG2	liver
13	chr3:42808000-42814000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:42808000-42814200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:42808800-42813200	Weak transcription	Monocytes-CD14+_RO01746	blood

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