Variant report

Variant	rs12996425
Chromosome Location	chr2:40636517-40636518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10490043	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13031545	1.00[CEU][hapmap]
rs13031785	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap]
rs13031843	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap]
rs13031849	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap]
rs13035085	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs17025926	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17025999	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs17026001	1.00[CEU][hapmap]
rs17026005	1.00[CEU][hapmap]
rs17026009	1.00[CEU][hapmap]
rs17026011	1.00[CEU][hapmap]
rs17026012	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs17026014	1.00[CEU][hapmap]
rs17026018	1.00[CEU][hapmap]
rs2041759	0.84[ASN][1000 genomes]
rs35920920	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35946417	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4993292	0.80[CHD][hapmap]
rs71439299	0.89[EUR][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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40623600-40655000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:40628400-40636800	Weak transcription	Right Ventricle	heart
3	chr2:40631400-40636600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:40631800-40639000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:40632600-40636800	Weak transcription	Fetal Brain Male	brain
6	chr2:40633000-40636800	Weak transcription	Brain Anterior Caudate	brain
7	chr2:40633000-40639200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:40633200-40639400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:40633600-40637200	Enhancers	Dnd41	blood
10	chr2:40634000-40637400	Enhancers	Colon Smooth Muscle	Colon
11	chr2:40634000-40639200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:40634600-40637000	Enhancers	Adipose Nuclei	Adipose
13	chr2:40634800-40644800	Weak transcription	Left Ventricle	heart
14	chr2:40634800-40645800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:40635200-40639600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:40635800-40639200	Weak transcription	HSMM	muscle
17	chr2:40635800-40639600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:40635800-40639800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:40635800-40643800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:40635800-40652600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:40636000-40639600	Weak transcription	NHDF-Ad	bronchial
22	chr2:40636000-40645600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:40636200-40636800	Weak transcription	Osteobl	bone
24	chr2:40636200-40646000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:40636400-40636600	Flanking Active TSS	Fetal Heart	heart
26	chr2:40636400-40636600	Enhancers	Stomach Smooth Muscle	stomach

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