Variant report

Variant	rs12469092
Chromosome Location	chr2:113363950-113363951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113356920..113360404-chr2:113360681..113365299,5	MCF-7	breast:
2	chr2:113361529..113364107-chr2:113384618..113387242,2	K562	blood:
3	chr2:113344320..113346442-chr2:113363758..113365916,2	MCF-7	breast:
4	chr2:113362689..113364237-chr2:113407440..113409332,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10171686	0.93[ASN][1000 genomes]
rs10190108	0.91[ASN][1000 genomes]
rs11691929	0.84[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11694460	0.93[ASN][1000 genomes]
rs11694966	0.91[ASN][1000 genomes]
rs12477807	0.98[ASN][1000 genomes]
rs12611573	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12613849	0.85[ASN][1000 genomes]
rs3849317	0.89[JPT][hapmap]
rs3961913	0.93[ASN][1000 genomes]
rs4848284	0.89[JPT][hapmap]
rs6748577	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6749723	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6757781	0.89[JPT][hapmap]
rs7594007	0.84[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7606487	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs934748	0.82[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs934749	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12469092	AC079922.3	cis	Heart Left Ventricle	GTEx
rs12469092	LOC653596	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113346800-113374600	Weak transcription	Ovary	ovary
2	chr2:113348600-113383600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:113348800-113364000	Weak transcription	Fetal Stomach	stomach
4	chr2:113349000-113384000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:113352200-113364800	Weak transcription	Primary T cells from cord blood	blood
6	chr2:113357000-113371800	Weak transcription	Gastric	stomach
7	chr2:113357800-113375200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:113357800-113384200	Weak transcription	Pancreas	Pancrea
9	chr2:113358000-113365400	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:113358000-113371800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:113358000-113384000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:113358400-113364600	Enhancers	Placenta	Placenta
13	chr2:113358600-113364400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:113359600-113364000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:113359600-113371800	Weak transcription	Brain Germinal Matrix	brain
16	chr2:113359800-113365200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:113359800-113372000	Weak transcription	Fetal Brain Female	brain
18	chr2:113363600-113364600	Enhancers	Stomach Mucosa	stomach
19	chr2:113363600-113364800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:113363800-113364000	Flanking Active TSS	Liver	Liver
21	chr2:113363800-113364000	Enhancers	HSMMtube	muscle
22	chr2:113363800-113364200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:113363800-113364600	Enhancers	Fetal Lung	lung
24	chr2:113363800-113364600	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr2:113363800-113364800	Enhancers	Duodenum Mucosa	Duodenum

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