Variant report

Variant	rs2929154
Chromosome Location	chr15:79048551-79048552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79047462..79049976-chr15:79054585..79057196,2	K562	blood:

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1045130	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1964562	0.84[EUR][1000 genomes]
rs2046143	0.83[EUR][1000 genomes]
rs34019568	0.87[EUR][1000 genomes]
rs59414039	0.85[EUR][1000 genomes]

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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2929154	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs2929154	CHRNA5	cis	Muscle Skeletal	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79040600-79060000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:79042800-79055400	Enhancers	Right Ventricle	heart
3	chr15:79043400-79048600	Weak transcription	Brain Angular Gyrus	brain
4	chr15:79043400-79049200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:79043400-79049200	Weak transcription	NHLF	lung
6	chr15:79043400-79049400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:79043400-79049600	Weak transcription	Pancreas	Pancrea
8	chr15:79043600-79048600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:79043600-79049600	Weak transcription	Colonic Mucosa	Colon
10	chr15:79043600-79049800	Weak transcription	Fetal Brain Female	brain
11	chr15:79043600-79077800	Weak transcription	Brain Germinal Matrix	brain
12	chr15:79043800-79048600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:79043800-79049200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:79043800-79049200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:79043800-79049200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:79043800-79049600	Weak transcription	Lung	lung
17	chr15:79043800-79052000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:79043800-79053400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:79044000-79049200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:79044000-79049200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:79044000-79049200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:79044000-79049600	Weak transcription	Stomach Mucosa	stomach
23	chr15:79044000-79050000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr15:79044000-79052600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr15:79044200-79049200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:79044200-79049200	Weak transcription	Fetal Thymus	thymus
27	chr15:79044200-79059000	Enhancers	Fetal Muscle Trunk	muscle
28	chr15:79044400-79049400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:79045000-79055800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:79045000-79059000	Enhancers	Fetal Muscle Leg	muscle
31	chr15:79045200-79049200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr15:79045600-79049400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:79046000-79049200	Enhancers	HSMM	muscle
34	chr15:79046200-79049200	Weak transcription	Spleen	Spleen
35	chr15:79046200-79054600	Enhancers	Fetal Heart	heart
36	chr15:79046400-79063200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:79046600-79049400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:79046800-79048600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr15:79046800-79049200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:79046800-79050200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:79047000-79053200	Enhancers	Stomach Smooth Muscle	stomach
42	chr15:79047200-79053600	Enhancers	NHDF-Ad	bronchial
43	chr15:79047200-79054600	Enhancers	HSMMtube	muscle
44	chr15:79047400-79048800	Enhancers	Psoas Muscle	Psoas
45	chr15:79047400-79049400	Weak transcription	Ovary	ovary
46	chr15:79047600-79048600	Weak transcription	Left Ventricle	heart
47	chr15:79047600-79049200	Weak transcription	Right Atrium	heart
48	chr15:79047600-79049600	Weak transcription	Fetal Lung	lung
49	chr15:79048000-79049200	Enhancers	Osteobl	bone
50	chr15:79048000-79050200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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