Variant report

Variant	rs682930
Chromosome Location	chr13:54824451-54824452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12429973	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12430260	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604306	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17667588	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17667614	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050378	0.82[EUR][1000 genomes]
rs2152084	0.83[EUR][1000 genomes]
rs2576147	0.92[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2782502	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2784566	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs2784567	1.00[CEU][hapmap]
rs2784568	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs2818222	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2818223	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2818224	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4883886	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883887	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4884928	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57804893	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684299	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795647	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795649	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs933101	0.92[CEU][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	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	nsv561701	chr13:54711276-54826104	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1051063	chr13:54777487-54997866	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv541778	chr13:54777487-54997866	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1046376	chr13:54785036-54827801	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv471132	chr13:54788842-54885744	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54822800-54835600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:54823800-54824800	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr13:54823800-54824800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr13:54823800-54825600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr13:54824000-54824600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr13:54824000-54824600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr13:54824000-54824800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr13:54824000-54825200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr13:54824200-54824600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links