Variant report

Variant	rs12908466
Chromosome Location	chr15:56126062-56126063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10518823	0.85[EUR][1000 genomes]
rs1104845	0.84[EUR][1000 genomes]
rs1104848	0.88[EUR][1000 genomes]
rs12898478	0.85[EUR][1000 genomes]
rs12899701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12906245	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12906350	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12908286	0.96[EUR][1000 genomes]
rs12911101	0.96[EUR][1000 genomes]
rs12913220	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17819270	0.84[EUR][1000 genomes]
rs1912397	0.85[EUR][1000 genomes]
rs1912403	0.84[EUR][1000 genomes]
rs2899593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34223710	0.81[EUR][1000 genomes]
rs34333169	0.96[EUR][1000 genomes]
rs34727807	0.85[EUR][1000 genomes]
rs34995202	0.85[EUR][1000 genomes]
rs35142499	0.81[EUR][1000 genomes]
rs35313340	0.96[EUR][1000 genomes]
rs35759462	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66857236	0.85[EUR][1000 genomes]
rs67046147	0.84[EUR][1000 genomes]
rs67825863	0.85[EUR][1000 genomes]
rs7172454	0.84[EUR][1000 genomes]
rs8033157	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs933997	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56095800-56128600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:56106000-56131200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:56112600-56133600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:56114600-56128200	Weak transcription	Esophagus	oesophagus
5	chr15:56115400-56148000	Weak transcription	Ovary	ovary
6	chr15:56115800-56129800	Weak transcription	Hela-S3	cervix
7	chr15:56116400-56129000	Weak transcription	NHLF	lung
8	chr15:56116400-56129600	Weak transcription	NHDF-Ad	bronchial
9	chr15:56116400-56133400	Weak transcription	Fetal Lung	lung
10	chr15:56116600-56150600	Weak transcription	Right Ventricle	heart
11	chr15:56116800-56162200	Weak transcription	Fetal Heart	heart
12	chr15:56117600-56131200	Weak transcription	Small Intestine	intestine
13	chr15:56118600-56151000	Weak transcription	Fetal Kidney	kidney
14	chr15:56118800-56147000	Weak transcription	Gastric	stomach
15	chr15:56118800-56149200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:56118800-56151400	Weak transcription	Brain Anterior Caudate	brain
17	chr15:56119200-56133000	Weak transcription	Primary T cells from cord blood	blood
18	chr15:56119400-56134800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:56120000-56126200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:56120000-56136800	Strong transcription	Liver	Liver
21	chr15:56120000-56144800	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:56120000-56147800	Weak transcription	HepG2	liver
23	chr15:56120200-56126400	Strong transcription	Osteobl	bone
24	chr15:56120600-56127600	Weak transcription	Lung	lung
25	chr15:56120600-56146600	Weak transcription	Pancreas	Pancrea
26	chr15:56120800-56126600	Weak transcription	Psoas Muscle	Psoas
27	chr15:56120800-56147200	Weak transcription	Thymus	Thymus
28	chr15:56121200-56147200	Weak transcription	Spleen	Spleen
29	chr15:56121600-56126400	Strong transcription	Placenta	Placenta
30	chr15:56121800-56126200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:56121800-56126200	Strong transcription	HSMMtube	muscle
32	chr15:56121800-56135600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:56122000-56136600	Strong transcription	Fetal Intestine Large	intestine
34	chr15:56122200-56129000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:56122200-56135400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:56122200-56136000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:56122400-56128000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:56122400-56136800	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:56122400-56145200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr15:56122600-56134200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr15:56122600-56152000	Weak transcription	Fetal Thymus	thymus
42	chr15:56122600-56153800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr15:56122600-56154800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr15:56122600-56156600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:56122800-56126200	Weak transcription	NHEK	skin
46	chr15:56122800-56129600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:56122800-56132600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:56122800-56134800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:56122800-56141600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr15:56122800-56147200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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