Variant report

Variant	rs360808
Chromosome Location	chr2:62927475-62927476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:62926107..62929773-chr2:62930954..62937858,8	K562	blood:
2	chr2:62924218..62929321-chr2:62929371..62934209,7	MCF-7	breast:
3	chr2:62919969..62928061-chr2:62929936..62935727,8	K562	blood:
4	chr2:62925529..62928377-chr2:62930964..62933788,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10181359	0.81[ASN][1000 genomes]
rs10184918	0.84[ASN][1000 genomes]
rs11682530	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs11688816	0.85[CHD][hapmap]
rs12713469	0.84[CEU][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs12989754	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs13013218	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs13410889	0.84[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs1420018	0.84[CHB][hapmap]
rs1553832	0.84[CHB][hapmap]
rs189671	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs2136737	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs2430388	0.85[CHD][hapmap]
rs2539981	0.81[ASN][1000 genomes]
rs2710638	0.84[CHD][hapmap]
rs360797	0.82[CHD][hapmap]
rs360799	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs360800	0.84[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs360801	0.84[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs360804	0.84[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs360807	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs4461246	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs4671448	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7573756	0.88[CHD][hapmap]
rs7591708	0.96[CEU][hapmap];0.87[GIH][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs360808	COMMD1	cis	cerebellum	SCAN
rs360808	MDH1	cis	cerebellum	SCAN
rs360808	WDPCP	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62926000-62927600	Active TSS	Adipose Nuclei	Adipose
2	chr2:62926000-62930400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:62926200-62930600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:62926400-62929200	Active TSS	Liver	Liver
5	chr2:62926400-62931800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:62927000-62930800	Weak transcription	HepG2	liver
7	chr2:62927400-62930200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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