Variant report

Variant	rs6544336
Chromosome Location	chr2:40627712-40627713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12328635	0.92[EUR][1000 genomes]
rs6544337	0.84[CEU][hapmap];0.85[CHD][hapmap];0.80[AMR][1000 genomes]
rs6730958	0.83[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6544336	MTA3	cis	parietal	SCAN
rs6544336	EIF2AK2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40622200-40635600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:40622800-40627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:40622800-40630400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:40622800-40630400	Weak transcription	Psoas Muscle	Psoas
5	chr2:40623000-40627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:40623000-40630400	Weak transcription	Fetal Brain Male	brain
7	chr2:40623000-40630800	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:40623000-40634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:40623600-40629800	Weak transcription	Brain Germinal Matrix	brain
10	chr2:40623600-40635000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:40623600-40655000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:40624200-40633600	Weak transcription	Dnd41	blood
13	chr2:40624800-40627800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:40625400-40630600	Weak transcription	Fetal Brain Female	brain
15	chr2:40625400-40631800	Weak transcription	Right Atrium	heart
16	chr2:40625600-40628000	Enhancers	Fetal Heart	heart
17	chr2:40626400-40628400	Enhancers	Left Ventricle	heart
18	chr2:40626400-40628400	Enhancers	Right Ventricle	heart
19	chr2:40627200-40628200	Enhancers	Fetal Intestine Small	intestine
20	chr2:40627200-40628400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr2:40627400-40627800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr2:40627400-40628000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr2:40627400-40628200	Enhancers	Fetal Intestine Large	intestine
24	chr2:40627400-40628400	Enhancers	Brain Anterior Caudate	brain
25	chr2:40627400-40629400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr2:40627400-40632800	Enhancers	HMEC	breast
27	chr2:40627400-40633000	Enhancers	NH-A	brain
28	chr2:40627600-40627800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr2:40627600-40627800	Flanking Active TSS	NHDF-Ad	bronchial
30	chr2:40627600-40628000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:40627600-40628000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:40627600-40628000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:40627600-40628000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:40627600-40628000	Enhancers	Ovary	ovary
35	chr2:40627600-40628000	Flanking Active TSS	HUVEC	blood vessel
36	chr2:40627600-40628000	Flanking Active TSS	Osteobl	bone
37	chr2:40627600-40628200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr2:40627600-40628200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:40627600-40628200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:40627600-40628200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:40627600-40628200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:40627600-40628200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:40627600-40628200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr2:40627600-40628200	Enhancers	Aorta	Aorta
45	chr2:40627600-40628200	Enhancers	Placenta	Placenta
46	chr2:40627600-40628200	Enhancers	Lung	lung
47	chr2:40627600-40628200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr2:40627600-40628200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr2:40627600-40628200	Enhancers	HSMMtube	muscle
50	chr2:40627600-40628400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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