Variant report

Variant	rs6580545
Chromosome Location	chr5:147713645-147713646
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10035818	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10036053	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10037318	0.86[EUR][1000 genomes]
rs10044054	0.94[CEU][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10050560	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051223	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs10055430	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs10057472	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10060180	0.83[EUR][1000 genomes]
rs10060753	0.80[CEU][hapmap]
rs10068891	0.89[CEU][hapmap];0.96[MKK][hapmap];0.93[EUR][1000 genomes]
rs10072817	0.87[EUR][1000 genomes]
rs10072958	0.95[CEU][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs10077690	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs10476892	0.94[EUR][1000 genomes]
rs10477374	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10515610	0.86[EUR][1000 genomes]
rs11168046	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12516267	0.88[EUR][1000 genomes]
rs12519039	0.87[EUR][1000 genomes]
rs12521065	0.95[CEU][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs12717971	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12717973	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs13153619	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13157347	0.87[EUR][1000 genomes]
rs13158948	0.84[EUR][1000 genomes]
rs13176114	0.93[EUR][1000 genomes]
rs13358385	0.87[EUR][1000 genomes]
rs1345741	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1363704	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363705	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1363707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1422968	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1422970	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1422976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1422977	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1582519	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17719578	0.93[EUR][1000 genomes]
rs17719662	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719763	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17719873	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17720155	0.83[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs17776554	0.87[EUR][1000 genomes]
rs17776674	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17776882	0.89[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1862430	0.93[EUR][1000 genomes]
rs1862431	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984789	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2112761	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[ASN][1000 genomes]
rs2161432	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2216653	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2400509	0.95[CEU][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs2400510	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs28442279	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2895761	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34001290	0.95[EUR][1000 genomes]
rs34163281	0.93[EUR][1000 genomes]
rs35006442	0.81[EUR][1000 genomes]
rs35700061	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35792476	0.93[EUR][1000 genomes]
rs3749689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749690	0.95[CEU][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs3925019	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4406123	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4599524	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs4599526	0.83[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4639213	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4705247	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705248	0.95[CEU][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs4705249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705251	0.87[EUR][1000 genomes]
rs4705252	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4705253	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6580542	0.93[EUR][1000 genomes]
rs6580544	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580548	0.93[EUR][1000 genomes]
rs6860261	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6861078	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs6865036	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6865972	0.95[EUR][1000 genomes]
rs6866106	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6875252	0.93[EUR][1000 genomes]
rs6875795	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6876308	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6876982	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs6882932	0.92[EUR][1000 genomes]
rs6886203	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891724	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6892647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893378	0.95[EUR][1000 genomes]
rs6894032	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7712350	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7713986	0.93[EUR][1000 genomes]
rs7716578	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7722458	0.86[EUR][1000 genomes]
rs7728004	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7729309	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7730707	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731526	0.87[EUR][1000 genomes]
rs7734458	0.95[CEU][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs7736019	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7736728	0.94[EUR][1000 genomes]
rs9325094	0.86[EUR][1000 genomes]
rs9325096	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9784645	0.91[EUR][1000 genomes]
rs999741	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv599945	chr5:147649181-147720487	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6580545	SPINK7	cis	uninvolved skin	skin_eQTL
rs6580545	SPINK9	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147709400-147749200	Weak transcription	Psoas Muscle	Psoas
2	chr5:147711800-147714200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:147713000-147728800	Weak transcription	Aorta	Aorta
4	chr5:147713400-147721800	Weak transcription	Liver	Liver

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