Variant report

Variant	rs6499984
Chromosome Location	chr16:58844113-58844114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11076259	0.87[EUR][1000 genomes]
rs11076260	0.87[EUR][1000 genomes]
rs12325516	0.86[EUR][1000 genomes]
rs12709012	0.88[EUR][1000 genomes]
rs1369933	0.87[EUR][1000 genomes]
rs1369934	0.87[EUR][1000 genomes]
rs1436427	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595180	0.87[EUR][1000 genomes]
rs1616072	0.86[EUR][1000 genomes]
rs1618602	0.88[EUR][1000 genomes]
rs1624301	0.87[EUR][1000 genomes]
rs1626006	0.87[EUR][1000 genomes]
rs1646265	0.87[EUR][1000 genomes]
rs1646268	0.84[EUR][1000 genomes]
rs1646269	0.84[EUR][1000 genomes]
rs1646274	0.86[EUR][1000 genomes]
rs1646275	0.85[EUR][1000 genomes]
rs1646278	0.87[EUR][1000 genomes]
rs1646279	0.87[EUR][1000 genomes]
rs1646280	0.86[EUR][1000 genomes]
rs1646281	0.88[EUR][1000 genomes]
rs1646282	0.85[EUR][1000 genomes]
rs1646284	0.87[EUR][1000 genomes]
rs1646285	0.87[EUR][1000 genomes]
rs1646286	0.87[EUR][1000 genomes]
rs1646287	0.87[EUR][1000 genomes]
rs1646288	0.87[EUR][1000 genomes]
rs1657161	0.84[EUR][1000 genomes]
rs1657163	0.85[EUR][1000 genomes]
rs1657164	0.86[EUR][1000 genomes]
rs1657167	0.86[EUR][1000 genomes]
rs1657169	0.83[EUR][1000 genomes]
rs1657171	0.83[EUR][1000 genomes]
rs166290	0.81[EUR][1000 genomes]
rs191783	0.87[EUR][1000 genomes]
rs2164515	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2432621	0.86[EUR][1000 genomes]
rs2432622	0.85[EUR][1000 genomes]
rs2575374	0.85[EUR][1000 genomes]
rs257624	0.87[EUR][1000 genomes]
rs257627	0.87[EUR][1000 genomes]
rs257628	0.87[EUR][1000 genomes]
rs257629	0.88[EUR][1000 genomes]
rs4238801	0.85[EUR][1000 genomes]
rs4315316	0.88[EUR][1000 genomes]
rs4427787	0.94[EUR][1000 genomes]
rs4538000	0.85[EUR][1000 genomes]
rs4575523	0.85[EUR][1000 genomes]
rs4784977	0.85[EUR][1000 genomes]
rs4784982	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6499985	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6499986	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7184377	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7194961	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs727484	0.87[EUR][1000 genomes]
rs72792430	0.85[EUR][1000 genomes]
rs8044542	0.86[EUR][1000 genomes]
rs8045466	0.88[EUR][1000 genomes]
rs8046154	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8049462	0.88[EUR][1000 genomes]
rs8051078	0.88[EUR][1000 genomes]
rs8054414	0.86[EUR][1000 genomes]
rs8060717	0.87[EUR][1000 genomes]
rs8060721	0.87[EUR][1000 genomes]
rs899375	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9302706	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9937713	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6499984	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs6499984	GOT2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58841400-58844400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr16:58843600-58847800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr16:58843600-58848400	Weak transcription	NHEK	skin

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