Variant report

Variant	rs2590549
Chromosome Location	chr13:94119685-94119686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1323989	0.85[ASN][1000 genomes]
rs1359198	0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs1408211	0.85[ASN][1000 genomes]
rs1445266	0.86[ASN][1000 genomes]
rs1445271	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1445272	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1445273	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1445275	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17234460	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1900050	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924383	0.88[ASN][1000 genomes]
rs1947077	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1947079	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980727	0.82[CHB][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.83[ASN][1000 genomes]
rs1987681	0.84[ASN][1000 genomes]
rs1987682	0.80[ASN][1000 genomes]
rs2038727	0.91[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs2590552	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2762082	0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.86[ASN][1000 genomes]
rs2762092	0.86[ASN][1000 genomes]
rs2813618	0.85[ASN][1000 genomes]
rs2813619	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2813620	0.86[ASN][1000 genomes]
rs2813621	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2813623	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2813627	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2813628	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2813631	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2813636	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999497	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2999500	0.86[ASN][1000 genomes]
rs4771875	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs4773745	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs4773746	0.85[ASN][1000 genomes]
rs4773747	0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.87[ASN][1000 genomes]
rs72640517	0.89[ASN][1000 genomes]
rs7329539	0.81[CHB][hapmap]
rs7338402	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs876808	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs895193	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs895194	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9301877	0.83[MEX][hapmap]
rs9301881	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9524051	0.82[ASN][1000 genomes]
rs9524053	0.85[ASN][1000 genomes]
rs9524058	0.83[ASN][1000 genomes]
rs9524061	0.86[ASN][1000 genomes]
rs9524070	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9524075	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556289	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9556291	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9561336	0.83[MEX][hapmap]
rs9561340	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9561346	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9561347	0.88[ASN][1000 genomes]
rs973302	0.86[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs974542	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974543	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974544	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs996460	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs996461	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs996462	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs996463	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv530636	chr13:93997311-94281707	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916039	chr13:94035909-94191105	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv562749	chr13:94083352-94263206	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv900920	chr13:94088707-94151937	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv1842896	chr13:94095160-94153194	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv900921	chr13:94105666-94157481	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv900922	chr13:94105666-94281492	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94108200-94120400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:94119600-94120200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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