Variant report

Variant	rs12999886
Chromosome Location	chr2:40640101-40640102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13031545	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13031785	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13031843	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13031849	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13035085	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17025999	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17026001	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17026003	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17026005	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17026009	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17026011	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17026012	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17026014	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17026018	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34038561	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34682370	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35321042	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35478019	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35797248	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35923316	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4993292	0.82[ASN][1000 genomes]
rs57193459	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61629255	0.86[EUR][1000 genomes]
rs71439297	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71439298	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71439299	0.84[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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40623600-40655000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:40634800-40644800	Weak transcription	Left Ventricle	heart
3	chr2:40634800-40645800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:40635800-40643800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:40635800-40652600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:40636000-40645600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:40636200-40646000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:40637000-40645600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:40637200-40645600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:40637200-40646000	Weak transcription	Right Ventricle	heart
11	chr2:40637200-40649000	Weak transcription	Dnd41	blood
12	chr2:40637400-40643600	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:40639000-40640200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:40639200-40640200	Flanking Active TSS	Fetal Heart	heart
15	chr2:40639200-40640200	Enhancers	NHEK	skin
16	chr2:40639800-40640200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:40639800-40643600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:40639800-40643600	Weak transcription	HMEC	breast
19	chr2:40639800-40643800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:40640000-40640600	Weak transcription	HSMM	muscle
21	chr2:40640000-40641400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:40640000-40645600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:40640000-40645800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:40640000-40646600	Weak transcription	Osteobl	bone
25	chr2:40640000-40647600	Weak transcription	NHLF	lung

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