Variant report

Variant	rs9661462
Chromosome Location	chr1:75051422-75051423
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10493546	0.92[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10789398	0.88[EUR][1000 genomes]
rs10789399	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs10890133	0.88[EUR][1000 genomes]
rs10890136	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890137	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap]
rs10890138	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs11210488	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11210489	0.89[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs11210490	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs11210492	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs12029405	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12074297	0.88[EUR][1000 genomes]
rs12117493	0.85[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs1340987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1378278	0.82[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs1424667	0.85[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs1563291	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs17548925	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1834189	0.85[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap]
rs3845350	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3845355	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap]
rs4123382	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4650002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6660278	0.85[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs6671066	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap]
rs6700243	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs6701034	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs72675359	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72675360	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv830248	chr1:74962391-75144458	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv870824	chr1:75019390-75125581	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9661462	FABP3	trans	lymphoblastoid	seeQTL
rs9661462	CRYZ	cis	parietal	SCAN
rs9661462	KRTAP10-3	trans	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75050600-75052000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:75050800-75051600	Enhancers	Liver	Liver

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