Variant report

Variant	rs12910629
Chromosome Location	chr15:45969780-45969781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12708404	1.00[ASN][1000 genomes]
rs12907319	1.00[ASN][1000 genomes]
rs12915009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733249	1.00[ASN][1000 genomes]
rs35267652	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35394591	1.00[ASN][1000 genomes]
rs35707605	1.00[ASN][1000 genomes]
rs6493163	1.00[ASN][1000 genomes]
rs7496542	1.00[ASN][1000 genomes]
rs8034672	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12910629	EIF3J	cis	cerebellum	SCAN
rs12910629	ZFYVE19	cis	cerebellum	SCAN
rs12910629	DISP2	cis	parietal	SCAN
rs12910629	VPS18	cis	cerebellum	SCAN
rs12910629	RHOV	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45949600-45976800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:45950600-45988400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:45950800-45986000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr15:45952800-45970200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:45953000-45984000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:45953200-45977600	Weak transcription	Stomach Mucosa	stomach
7	chr15:45953400-45974600	Weak transcription	HepG2	liver
8	chr15:45953400-45986200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr15:45954000-45980000	Weak transcription	Fetal Thymus	thymus
10	chr15:45954800-45981600	Weak transcription	Brain Substantia Nigra	brain
11	chr15:45956000-45970200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:45957400-45972200	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:45957400-45973400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:45957400-45981200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:45957400-45985800	Weak transcription	HSMMtube	muscle
16	chr15:45957800-45970400	Weak transcription	Osteobl	bone
17	chr15:45958400-45986400	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:45959600-45986200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:45960000-45970400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:45960000-45986000	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:45960200-45971200	Strong transcription	Colonic Mucosa	Colon
22	chr15:45960200-45987800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr15:45960400-45970800	Strong transcription	Left Ventricle	heart
24	chr15:45960400-45985200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:45960400-45985800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:45960400-45986200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr15:45960400-45987000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:45960400-45988200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr15:45960600-45970400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:45960600-45985800	Strong transcription	Primary T cells from cord blood	blood
31	chr15:45960600-45986000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr15:45960600-45986000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:45960600-45986600	Strong transcription	Primary B cells from cord blood	blood
34	chr15:45960600-45987200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:45960800-45970200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:45960800-45985600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:45960800-45987000	Strong transcription	Liver	Liver
38	chr15:45961400-45972800	Strong transcription	Fetal Intestine Large	intestine
39	chr15:45961600-45971200	Strong transcription	Lung	lung
40	chr15:45961800-45987000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr15:45962800-45976200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:45963000-45971400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:45963000-45982200	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:45963200-45971000	Strong transcription	Adipose Nuclei	Adipose
45	chr15:45963200-45984400	Weak transcription	Fetal Kidney	kidney
46	chr15:45963400-45970400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:45963600-45970600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:45963600-45971000	Strong transcription	Spleen	Spleen
49	chr15:45964800-45970600	Strong transcription	Rectal Smooth Muscle	rectum
50	chr15:45964800-45986000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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