Variant report

Variant	rs2590539
Chromosome Location	chr13:94171867-94171868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1318869	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1445246	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1445247	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948911	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948925	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948958	0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2389007	0.85[AFR][1000 genomes]
rs2590508	1.00[AMR][1000 genomes]
rs2590513	1.00[AMR][1000 genomes]
rs2590516	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590518	1.00[YRI][hapmap]
rs2590519	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590520	0.84[AFR][1000 genomes]
rs2590521	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590522	0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590524	0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590525	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590526	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590527	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs2590528	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590529	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590530	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590531	0.90[YRI][hapmap]
rs2590532	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590533	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590534	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590535	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs2590537	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590538	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590540	0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590541	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590542	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2813589	1.00[AMR][1000 genomes]
rs2813598	0.84[YRI][hapmap];0.99[AFR][1000 genomes]
rs2813599	0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2813600	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2813601	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2813602	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2813603	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2813604	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2813605	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2813607	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3908638	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6492666	0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7320003	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7322180	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7322574	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7326344	1.00[AMR][1000 genomes]
rs7328826	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7329040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7329041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7333593	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7338822	0.95[YRI][hapmap];1.00[AFR][1000 genomes]
rs74108582	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74108584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74108585	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7981908	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7982284	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7993697	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7999055	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs975827	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs976419	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs976420	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs976421	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
8	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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94161800-94176200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:94162800-94175800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:94163000-94174400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:94168800-94173600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr13:94168800-94178000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:94169200-94176200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr13:94170600-94172800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr13:94170800-94172200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:94171000-94174400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:94171200-94172800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr13:94171600-94172600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr13:94171600-94172600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr13:94171800-94172800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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