Variant report

Variant	rs6782577
Chromosome Location	chr3:49620770-49620771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1050088	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1060962	0.96[CEU][hapmap]
rs10640	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10865955	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11130192	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11130199	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs11130202	0.81[ASN][1000 genomes]
rs11130203	0.82[ASN][1000 genomes]
rs11706370	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11711485	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11712569	0.82[ASN][1000 genomes]
rs11713474	0.90[ASN][1000 genomes]
rs11715915	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11719996	0.82[ASN][1000 genomes]
rs11720264	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs11720458	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11919311	0.96[CEU][hapmap]
rs11922013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11926781	0.90[ASN][1000 genomes]
rs12330269	0.82[ASN][1000 genomes]
rs12489092	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs12636099	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13079082	0.82[ASN][1000 genomes]
rs1464566	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs1464567	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1464568	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap]
rs1568661	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1801143	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1826347	0.96[CEU][hapmap]
rs1873626	0.96[CEU][hapmap]
rs2005557	0.96[CEU][hapmap]
rs2131104	0.96[CEU][hapmap]
rs2131109	0.96[CEU][hapmap]
rs2312461	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2329020	0.96[CEU][hapmap]
rs34293138	0.82[ASN][1000 genomes]
rs34363169	0.82[ASN][1000 genomes]
rs34427167	0.90[ASN][1000 genomes]
rs35261698	0.82[ASN][1000 genomes]
rs35701831	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35999162	0.86[ASN][1000 genomes]
rs3811697	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs3870337	0.81[ASN][1000 genomes]
rs3870338	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs3877784	0.81[ASN][1000 genomes]
rs3924462	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs4241406	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4241408	0.80[AFR][1000 genomes]
rs4625	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4855836	0.81[ASN][1000 genomes]
rs4855839	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4855842	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4855852	0.96[CEU][hapmap]
rs4855855	0.89[AFR][1000 genomes]
rs4855859	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs4855861	0.81[ASN][1000 genomes]
rs4855864	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs4855873	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs4855877	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[YRI][hapmap]
rs4855881	0.96[CEU][hapmap]
rs4855884	0.96[CEU][hapmap]
rs56116382	0.86[ASN][1000 genomes]
rs6446272	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6766131	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6766581	0.82[ASN][1000 genomes]
rs6779524	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6784820	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap]
rs6787417	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6797664	0.82[ASN][1000 genomes]
rs6997	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7622302	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7633271	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7637665	0.92[AFR][1000 genomes]
rs7637999	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs7643845	0.81[ASN][1000 genomes]
rs7645445	0.81[AFR][1000 genomes]
rs7646366	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs885592	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap]
rs9814873	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9818590	0.82[ASN][1000 genomes]
rs9827021	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs9837027	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9841110	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs9850072	0.82[ASN][1000 genomes]
rs9853683	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9858280	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs9875617	1.00[CHB][hapmap];0.82[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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6782577	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs6782577	WDR6	cis	Nerve Tibial	GTEx
rs6782577	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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