Variant report

Variant	rs12477807
Chromosome Location	chr2:113359205-113359206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113358188..113360377-chr2:113398948..113401833,2	K562	blood:
2	chr2:113005402..113007381-chr2:113358555..113361343,2	K562	blood:
3	chr2:113356814..113361031-chr2:113482443..113485915,5	MCF-7	breast:
4	chr2:113358913..113360959-chr2:113401805..113405179,4	MCF-7	breast:
5	chr2:113356349..113359292-chr2:113483016..113484576,2	K562	blood:
6	chr2:113358735..113361704-chr2:113402110..113405649,3	K562	blood:
7	chr2:113350147..113353679-chr2:113358918..113360716,3	MCF-7	breast:
8	chr2:113356920..113360404-chr2:113360681..113365299,5	MCF-7	breast:
9	chr2:113356246..113359839-chr2:113408208..113412087,4	K562	blood:
10	chr2:113340607..113344636-chr2:113357649..113359870,4	MCF-7	breast:
11	chr2:113357797..113359633-chr2:113475754..113478612,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000125611	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10171686	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10190108	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11691929	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694460	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11694966	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12469092	0.98[ASN][1000 genomes]
rs12611573	0.88[ASN][1000 genomes]
rs12613849	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34725617	0.87[EUR][1000 genomes]
rs3961913	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6748577	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749723	0.92[ASN][1000 genomes]
rs7594007	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606487	0.93[ASN][1000 genomes]
rs934748	0.95[ASN][1000 genomes]
rs934749	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113344200-113360800	Weak transcription	Fetal Brain Male	brain
2	chr2:113346800-113374600	Weak transcription	Ovary	ovary
3	chr2:113347600-113363800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:113348600-113383600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:113348800-113364000	Weak transcription	Fetal Stomach	stomach
6	chr2:113349000-113384000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:113349400-113361400	Weak transcription	Thymus	Thymus
8	chr2:113352200-113364800	Weak transcription	Primary T cells from cord blood	blood
9	chr2:113355400-113363800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:113357000-113371800	Weak transcription	Gastric	stomach
11	chr2:113357400-113359400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:113357400-113359800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:113357400-113359800	Enhancers	HMEC	breast
14	chr2:113357400-113359800	Enhancers	NHEK	skin
15	chr2:113357600-113359600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:113357600-113359800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:113357800-113375200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:113357800-113384200	Weak transcription	Pancreas	Pancrea
19	chr2:113358000-113360400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:113358000-113360400	Weak transcription	HepG2	liver
21	chr2:113358000-113360600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:113358000-113361600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:113358000-113365400	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:113358000-113371800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:113358000-113384000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:113358200-113360200	Weak transcription	Liver	Liver
27	chr2:113358400-113364600	Enhancers	Placenta	Placenta
28	chr2:113358600-113359600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:113358600-113363800	Weak transcription	HSMMtube	muscle
30	chr2:113358600-113364400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:113358800-113359800	Strong transcription	Fetal Brain Female	brain
32	chr2:113359000-113359800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:113359200-113359600	Strong transcription	Brain Germinal Matrix	brain

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