Variant report

Variant	rs2784560
Chromosome Location	chr13:54699588-54699589
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10467530	0.80[AMR][1000 genomes]
rs12427903	0.97[EUR][1000 genomes]
rs12429828	0.97[EUR][1000 genomes]
rs12430260	0.89[EUR][1000 genomes]
rs1335979	0.88[AMR][1000 genomes]
rs1335980	0.85[AMR][1000 genomes]
rs1577577	1.00[EUR][1000 genomes]
rs17604306	0.89[EUR][1000 genomes]
rs17667588	0.87[EUR][1000 genomes]
rs17667614	0.87[EUR][1000 genomes]
rs1855847	1.00[EUR][1000 genomes]
rs1889824	1.00[EUR][1000 genomes]
rs1932503	0.88[AMR][1000 genomes]
rs1960782	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1984140	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1984141	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2005372	0.88[AMR][1000 genomes]
rs2050378	0.95[EUR][1000 genomes]
rs2050534	0.88[AMR][1000 genomes]
rs2050535	0.88[AMR][1000 genomes]
rs2050536	0.82[AMR][1000 genomes]
rs2065822	1.00[EUR][1000 genomes]
rs2152084	0.93[EUR][1000 genomes]
rs2152503	0.88[AMR][1000 genomes]
rs2184678	0.88[AMR][1000 genomes]
rs2408992	0.85[AMR][1000 genomes]
rs2408993	0.88[AMR][1000 genomes]
rs2408994	0.85[AMR][1000 genomes]
rs2408995	0.88[AMR][1000 genomes]
rs2576122	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576124	1.00[EUR][1000 genomes]
rs2576125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576126	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576127	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576128	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2576129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576131	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576135	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2576136	1.00[EUR][1000 genomes]
rs2576147	0.96[EUR][1000 genomes]
rs2784555	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2784556	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2784559	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2784561	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2784562	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2784564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2784566	0.85[CEU][hapmap];1.00[EUR][1000 genomes]
rs2784567	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2784568	0.85[CEU][hapmap];1.00[EUR][1000 genomes]
rs2784569	0.92[EUR][1000 genomes]
rs2784572	1.00[EUR][1000 genomes]
rs4883848	0.88[AMR][1000 genomes]
rs4883850	0.88[AMR][1000 genomes]
rs4884867	0.88[AMR][1000 genomes]
rs4884928	0.84[EUR][1000 genomes]
rs5002542	0.88[AMR][1000 genomes]
rs5002543	0.88[AMR][1000 genomes]
rs57804893	0.89[EUR][1000 genomes]
rs6561766	0.81[AMR][1000 genomes]
rs7326186	0.86[AMR][1000 genomes]
rs7326388	0.88[AMR][1000 genomes]
rs7335475	0.88[AMR][1000 genomes]
rs7984593	0.88[AMR][1000 genomes]
rs7985320	0.88[AMR][1000 genomes]
rs7986212	0.88[AMR][1000 genomes]
rs7991755	0.88[AMR][1000 genomes]
rs8001182	0.86[AMR][1000 genomes]
rs878942	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878943	0.88[AMR][1000 genomes]
rs933101	0.96[EUR][1000 genomes]
rs9536639	0.88[AMR][1000 genomes]
rs988527	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs988528	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][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	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
4	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
5	nsv9071	chr13:54697730-54701031	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54689000-54706000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:54689400-54700000	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr13:54691800-54706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr13:54692600-54705000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr13:54693800-54700000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:54696200-54700400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr13:54697200-54700600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr13:54697600-54702600	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr13:54698800-54700800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr13:54698800-54701000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr13:54699000-54701600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr13:54699200-54701400	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links