Variant report

Variant	rs6747380
Chromosome Location	chr2:56587749-56587750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10172020	0.91[CHB][hapmap]
rs10175691	0.91[CHB][hapmap]
rs10200604	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.81[EUR][1000 genomes]
rs11886381	0.92[CHB][hapmap]
rs11893331	0.86[EUR][1000 genomes]
rs13021782	0.85[CHB][hapmap]
rs13389344	0.83[CHB][hapmap]
rs1549031	0.83[CHB][hapmap]
rs17047851	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17047854	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17047856	0.92[CHB][hapmap]
rs17268785	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671278	0.91[CHB][hapmap]
rs4672106	0.91[CHB][hapmap]
rs4672109	0.81[JPT][hapmap]
rs4672110	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs56140649	0.85[EUR][1000 genomes]
rs6545572	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[EUR][1000 genomes]
rs6545574	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704684	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714635	0.85[CHB][hapmap]
rs6735003	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.85[EUR][1000 genomes]
rs6748308	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs6756427	0.92[EUR][1000 genomes]
rs6760269	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs7355411	0.91[CHB][hapmap]
rs7562381	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.86[EUR][1000 genomes]
rs7566597	0.91[CHB][hapmap]
rs7573049	0.86[EUR][1000 genomes]
rs7602657	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530516	chr2:56447922-56633505	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv874170	chr2:56496589-56590865	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv834093	chr2:56538097-56708677	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1004449	chr2:56538460-56715861	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv874171	chr2:56545845-56727178	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv582032	chr2:56551074-56599354	Weak transcription Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Menarche (age at onset)	25231870	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6747380	AVPI1	cis	Liver	GTEx
rs6747380	AVPI1	trans	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56576000-56603000	Weak transcription	HSMM	muscle
2	chr2:56576000-56613200	Weak transcription	Left Ventricle	heart
3	chr2:56586400-56587800	Enhancers	Pancreatic Islets	Pancreatic Islet

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