Variant report

Variant	rs2260462
Chromosome Location	chr13:54692032-54692033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1335979	0.87[ASN][1000 genomes]
rs1335980	0.88[ASN][1000 genomes]
rs1537644	0.83[EUR][1000 genomes]
rs1932503	0.87[ASN][1000 genomes]
rs2005372	0.87[ASN][1000 genomes]
rs2050534	0.87[ASN][1000 genomes]
rs2050535	0.87[ASN][1000 genomes]
rs2050536	0.87[ASN][1000 genomes]
rs2152503	0.83[ASN][1000 genomes]
rs2184678	0.87[ASN][1000 genomes]
rs2261357	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs2261359	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs2261365	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs2408992	0.88[ASN][1000 genomes]
rs2408993	0.87[ASN][1000 genomes]
rs2408994	0.87[ASN][1000 genomes]
rs2408995	0.87[ASN][1000 genomes]
rs2576113	0.89[EUR][1000 genomes]
rs2576118	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576132	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2576143	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576144	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2782515	0.89[EUR][1000 genomes]
rs2782517	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2782518	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2784552	0.86[JPT][hapmap]
rs2784558	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs484366	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4883848	0.87[ASN][1000 genomes]
rs4883850	0.87[ASN][1000 genomes]
rs4884867	0.87[ASN][1000 genomes]
rs5002542	0.87[ASN][1000 genomes]
rs5002543	0.87[ASN][1000 genomes]
rs515604	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs518647	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs520026	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs538663	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs574751	0.89[EUR][1000 genomes]
rs632059	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs636911	0.96[EUR][1000 genomes]
rs664745	0.89[EUR][1000 genomes]
rs681748	0.89[EUR][1000 genomes]
rs688466	0.96[EUR][1000 genomes]
rs7326186	0.85[ASN][1000 genomes]
rs7326388	0.83[ASN][1000 genomes]
rs7335475	0.87[ASN][1000 genomes]
rs795635	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs795642	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs795643	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs795652	1.00[EUR][1000 genomes]
rs795653	0.96[EUR][1000 genomes]
rs795655	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs795656	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs797060	0.92[EUR][1000 genomes]
rs7984593	0.87[ASN][1000 genomes]
rs7985320	0.87[ASN][1000 genomes]
rs7986212	0.87[ASN][1000 genomes]
rs7991755	0.87[ASN][1000 genomes]
rs7993452	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8001182	0.87[ASN][1000 genomes]
rs812128	0.89[EUR][1000 genomes]
rs878943	0.87[ASN][1000 genomes]
rs9536639	0.87[ASN][1000 genomes]
rs988526	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3375545	chr13:54517432-54908108	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1049	chr13:54684354-54728981	Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv34795	chr13:54691999-54695928	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	esv2757533	chr13:54692032-54711236	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	esv2759938	chr13:54692032-54711236	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54683200-54698800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr13:54688600-54692200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:54688600-54699000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:54689000-54706000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:54689400-54700000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr13:54691800-54706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr13:54692000-54692200	Genic enhancers	H9 Cell Line	embryonic stem cell
8	chr13:54692000-54695400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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