Variant report

Variant	rs10840624
Chromosome Location	chr12:122301299-122301300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122239996..122242315-chr12:122299933..122302886,2	MCF-7	breast:
2	chr12:122239049..122240564-chr12:122299953..122302949,2	K562	blood:

Variant related genes	Relation type
ENSG00000139718	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10840622	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11043213	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11043216	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11043217	0.91[EUR][1000 genomes]
rs11043218	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11043219	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11043220	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs11043223	0.96[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs11043225	0.90[EUR][1000 genomes]
rs11043229	0.83[CHB][hapmap]
rs11043237	0.83[CHB][hapmap]
rs12825161	0.90[EUR][1000 genomes]
rs1610041	0.85[CEU][hapmap];0.83[CHB][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2167067	0.91[EUR][1000 genomes]
rs35599566	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35633723	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35892692	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3847694	0.83[CHB][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs6486780	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66611928	0.91[EUR][1000 genomes]
rs68055743	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7137218	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs7137708	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7313252	0.83[CHB][hapmap]
rs7958406	0.81[CHB][hapmap]
rs7969671	0.89[AMR][1000 genomes];0.98[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription 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 target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10840624	DIABLO	cis	parietal	SCAN
rs10840624	LOC338799	cis	parietal	SCAN
rs10840624	RP11-7M8.2	cis	Muscle Skeletal	GTEx
rs10840624	WDR66	cis	cerebellum	SCAN
rs10840624	HPD	cis	Muscle Skeletal	GTEx
rs10840624	HPD	cis	Heart Left Ventricle	GTEx
rs10840624	OASL	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122297000-122304200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:122297600-122304400	Weak transcription	NHDF-Ad	bronchial
3	chr12:122299600-122301400	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr12:122300200-122301400	Weak transcription	Adipose Nuclei	Adipose
5	chr12:122300200-122302000	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr12:122300200-122304600	Weak transcription	Osteobl	bone
7	chr12:122300200-122310800	Weak transcription	Placenta	Placenta
8	chr12:122300400-122304600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:122300400-122309400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:122301000-122301400	Enhancers	Pancreas	Pancrea
11	chr12:122301200-122301600	Enhancers	Liver	Liver
12	chr12:122301200-122301600	Enhancers	HepG2	liver

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