Variant report

Variant	rs2139629
Chromosome Location	chr2:50627597-50627598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10187911	0.83[JPT][hapmap]
rs10204268	0.91[ASN][1000 genomes]
rs10210298	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11903097	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053271	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12474009	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12475464	0.80[JPT][hapmap]
rs12616829	0.90[ASN][1000 genomes]
rs12616901	0.89[ASN][1000 genomes]
rs12620185	0.87[ASN][1000 genomes]
rs13404855	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13407780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1402121	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1520445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1543973	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17040490	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17040542	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs17040552	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs17040606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs1879320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1915170	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1915172	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1969351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1972311	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2176853	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2176854	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2176855	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2882692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4450643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4493303	0.86[JPT][hapmap]
rs4971557	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4971668	0.99[ASN][1000 genomes]
rs4971670	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs5019239	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6727675	0.88[ASN][1000 genomes]
rs7560420	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7560724	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7575728	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7599052	1.00[CHB][hapmap];1.00[JPT][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	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv948548	chr2:50569117-50695100	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50624400-50628600	Weak transcription	Stomach Mucosa	stomach
2	chr2:50624400-50629200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:50626000-50629000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:50626000-50629400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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