Variant report

Variant	rs997644
Chromosome Location	chr2:53867187-53867188
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10185375	0.85[JPT][hapmap]
rs10190578	0.81[GIH][hapmap]
rs10210726	0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs12612589	0.85[JPT][hapmap]
rs12612737	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12612895	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12613682	0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs12614610	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12617315	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12617360	0.86[EUR][1000 genomes]
rs12617668	0.80[EUR][1000 genomes]
rs12618833	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621635	0.86[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs13414183	0.81[GIH][hapmap]
rs17045125	0.83[EUR][1000 genomes]
rs17045215	0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs2009149	0.84[EUR][1000 genomes]
rs2058953	0.89[ASN][1000 genomes]
rs2287344	0.85[JPT][hapmap];0.82[TSI][hapmap]
rs2287345	0.85[JPT][hapmap]
rs2287512	0.90[CHD][hapmap];0.91[GIH][hapmap];0.86[ASN][1000 genomes]
rs2357491	0.84[ASW][hapmap];0.82[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2357492	0.86[ASN][1000 genomes]
rs35833242	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770401	0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs3770410	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770412	0.84[ASN][1000 genomes]
rs3770415	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821080	0.81[GIH][hapmap]
rs4361164	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56189833	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66684820	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6705484	0.80[CHD][hapmap]
rs67073722	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6714424	0.81[GIH][hapmap]
rs6716301	0.88[ASN][1000 genomes]
rs6760101	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68123661	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7595713	0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs991599	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs994484	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv874145	chr2:53772561-53867308	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv874146	chr2:53772561-53872803	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv874147	chr2:53772561-53886799	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2762637	chr2:53783253-53871596	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv527830	chr2:53785037-53867308	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1008117	chr2:53791985-53869651	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv535719	chr2:53791985-53869651	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53857400-53868600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:53865000-53868000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:53865000-53870000	Weak transcription	Fetal Brain Male	brain

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