Variant report

Variant	rs17581251
Chromosome Location	chr1:171232446-171232447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10399602	0.82[EUR][1000 genomes]
rs10399952	0.82[EUR][1000 genomes]
rs10798297	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10912672	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs10912673	0.90[ASN][1000 genomes]
rs10912713	0.82[EUR][1000 genomes]
rs10912714	0.82[EUR][1000 genomes]
rs10912723	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912736	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1126692	0.82[EUR][1000 genomes]
rs11484642	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11487396	0.81[EUR][1000 genomes]
rs12057955	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12058402	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12059179	0.81[EUR][1000 genomes]
rs12062692	1.00[CHB][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12068552	0.94[ASN][1000 genomes]
rs12070766	0.81[EUR][1000 genomes]
rs12072043	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12077231	0.94[ASN][1000 genomes]
rs12077755	0.81[EUR][1000 genomes]
rs12079141	0.94[ASN][1000 genomes]
rs12080449	0.94[ASN][1000 genomes]
rs12091482	0.82[EUR][1000 genomes]
rs12092985	0.82[EUR][1000 genomes]
rs12094878	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12141555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12354390	0.82[EUR][1000 genomes]
rs12726624	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729885	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.94[ASN][1000 genomes]
rs12730181	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12742008	0.94[ASN][1000 genomes]
rs12745080	0.81[EUR][1000 genomes]
rs12757839	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs13376631	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864302	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864387	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.94[ASN][1000 genomes]
rs2006986	0.81[EUR][1000 genomes]
rs2076322	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs2092311	1.00[CHB][hapmap]
rs2284131	1.00[CHB][hapmap]
rs28741369	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34118031	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34320519	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4607925	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.94[ASN][1000 genomes]
rs6670639	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6674596	0.83[EUR][1000 genomes]
rs742350	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs742351	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7512853	0.82[EUR][1000 genomes]
rs7519999	0.82[EUR][1000 genomes]
rs7539057	1.00[CHB][hapmap];0.86[TSI][hapmap];0.82[EUR][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17581251	VAMP4	cis	cerebellum	SCAN
rs17581251	FMO1	cis	cerebellum	SCAN
rs17581251	FMO4	cis	parietal	SCAN
rs17581251	FMO4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171228200-171232600	Weak transcription	Placenta	Placenta
2	chr1:171228200-171232600	Weak transcription	Fetal Stomach	stomach
3	chr1:171228400-171233000	Strong transcription	Fetal Intestine Large	intestine
4	chr1:171228600-171232800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:171228600-171233000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:171228600-171235200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:171228800-171233000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:171228800-171244400	Weak transcription	Fetal Kidney	kidney
9	chr1:171229200-171234600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:171229400-171235000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:171230600-171235000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:171230600-171236200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:171232200-171234200	Strong transcription	Fetal Intestine Small	intestine
14	chr1:171232400-171233200	Enhancers	Ovary	ovary
15	chr1:171232400-171233800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:171232400-171233800	Enhancers	Fetal Lung	lung
17	chr1:171232400-171234200	Enhancers	Fetal Muscle Leg	muscle

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