Variant report

Variant	rs2216007
Chromosome Location	chr2:40632095-40632096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10490042	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12328635	0.83[AFR][1000 genomes]
rs12614757	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4362610	0.85[AFR][1000 genomes]
rs59693719	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6732205	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7577611	0.90[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs9789765	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.96[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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873916	chr2:40607504-40649084	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1007027	chr2:40627475-40649916	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2216007	MTA3	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40622200-40635600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:40623000-40634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:40623600-40635000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:40623600-40655000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:40624200-40633600	Weak transcription	Dnd41	blood
6	chr2:40627400-40632800	Enhancers	HMEC	breast
7	chr2:40627400-40633000	Enhancers	NH-A	brain
8	chr2:40627600-40633000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:40627600-40633000	Enhancers	NHLF	lung
10	chr2:40627800-40632400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:40628000-40633000	Enhancers	Osteobl	bone
12	chr2:40628200-40633000	Enhancers	NHDF-Ad	bronchial
13	chr2:40628200-40633600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:40628400-40634000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:40628400-40634600	Weak transcription	Adipose Nuclei	Adipose
16	chr2:40628400-40636800	Weak transcription	Right Ventricle	heart
17	chr2:40629800-40633200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:40630400-40632200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:40630400-40632600	Enhancers	Fetal Brain Male	brain
20	chr2:40630400-40633000	Enhancers	Brain Germinal Matrix	brain
21	chr2:40630800-40633600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:40631000-40632400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr2:40631400-40632200	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:40631400-40632400	Flanking Active TSS	Fetal Heart	heart
25	chr2:40631400-40633200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:40631400-40635400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:40631400-40636400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:40631400-40636600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:40631600-40632800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr2:40631600-40634800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:40631600-40635400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:40631800-40632200	Active TSS	Brain Anterior Caudate	brain
33	chr2:40631800-40632200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr2:40631800-40632200	Flanking Active TSS	HSMM	muscle
35	chr2:40631800-40632200	Flanking Active TSS	HSMMtube	muscle
36	chr2:40631800-40632400	Active TSS	Brain Cingulate Gyrus	brain
37	chr2:40631800-40634000	Enhancers	Rectal Smooth Muscle	rectum
38	chr2:40631800-40639000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:40632000-40632200	Active TSS	Brain Hippocampus Middle	brain
40	chr2:40632000-40633000	Enhancers	Fetal Brain Female	brain
41	chr2:40632000-40633600	Weak transcription	Left Ventricle	heart
42	chr2:40632000-40633600	Weak transcription	Right Atrium	heart

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