Variant report

Variant	rs839540
Chromosome Location	chr2:212812060-212812061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10205607	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs12473131	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs12616932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12623434	0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs1402719	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2139936	0.90[AFR][1000 genomes]
rs2139937	0.90[AFR][1000 genomes]
rs2579980	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs2685006	0.98[ASN][1000 genomes]
rs2888037	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4673644	0.90[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs6435682	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6707590	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6744796	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs707284	0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs72935738	0.94[ASN][1000 genomes]
rs839499	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs839501	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs839504	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs839509	0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs839511	0.93[ASW][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs839512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs839515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839517	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs839518	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839519	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs839521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839522	0.98[ASN][1000 genomes]
rs839523	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.98[ASN][1000 genomes]
rs839525	0.93[ASW][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs839526	0.94[AFR][1000 genomes]
rs839527	0.90[AFR][1000 genomes]
rs839528	0.83[AFR][1000 genomes]
rs839530	0.87[ASW][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs839541	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860821	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs864528	0.98[ASN][1000 genomes]
rs990741	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34128	chr2:212581485-212857122	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv834525	chr2:212693190-212860356	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:212806800-212816400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:212811400-212812200	Enhancers	GM12878-XiMat	blood

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