Variant report

Variant	rs12054301
Chromosome Location	chr3:146116870-146116871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1054736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11707383	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715366	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1720242	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2120384	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs35102814	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35296568	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs35783134	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36067998	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4681324	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs487578	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs491900	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs498201	0.80[ASN][1000 genomes]
rs506974	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs512845	0.80[ASN][1000 genomes]
rs523849	0.94[CHB][hapmap]
rs524720	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs536619	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs536737	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs56111687	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563385	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs568302	0.94[CHB][hapmap]
rs575834	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs577842	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs62274675	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6764342	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs968634	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs968635	0.94[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536759	chr3:146087689-146123589	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1011893	chr3:146090110-146125010	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv877617	chr3:146096182-146172109	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877618	chr3:146096182-146192324	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877619	chr3:146106142-146172109	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	nsv877620	chr3:146109354-146172109	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146111800-146119400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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