Variant report

Variant	rs12664681
Chromosome Location	chr6:143359013-143359014
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIVEP2-2	chr6:143358126-143359214	ENSG00000229017.2
2	lnc-AIG1-5	chr6:143358752-143362819	NONHSAT115335

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11155277	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12660943	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12662675	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662882	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663085	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12663937	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664685	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12665506	0.82[MEX][hapmap]
rs1334477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1334478	0.91[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17590726	0.91[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17590859	0.82[MEX][hapmap]
rs1855560	0.82[EUR][1000 genomes]
rs1889462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2142936	0.82[EUR][1000 genomes]
rs2876540	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2876541	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35073854	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35569003	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761996	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3789782	0.86[CHB][hapmap]
rs3804526	0.86[CHB][hapmap]
rs3804527	0.86[CHB][hapmap]
rs3804528	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs3804530	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3827797	0.86[CHB][hapmap]
rs4896614	0.82[EUR][1000 genomes]
rs4896615	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59463222	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59873234	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59974378	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6905621	0.80[CHB][hapmap]
rs6936192	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs6938207	0.86[CHB][hapmap]
rs73777857	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7741073	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7743474	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7750571	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760119	0.82[MEX][hapmap]
rs7774011	0.86[CHB][hapmap]
rs7775419	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9321887	0.86[CHB][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs9321888	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs9321889	0.82[EUR][1000 genomes]
rs9399416	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs9403430	0.82[EUR][1000 genomes]
rs989325	1.00[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538459	chr6:143165802-143360098	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143356800-143360000	Weak transcription	GM12878-XiMat	blood
2	chr6:143356800-143377000	Weak transcription	HepG2	liver
3	chr6:143358000-143359200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:143358200-143359600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:143358600-143359200	Enhancers	HSMM	muscle
6	chr6:143359000-143360000	Weak transcription	K562	blood

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