Variant report

Variant	rs3934898
Chromosome Location	chr15:79055278-79055279
allele	C/T
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: 8 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1045130	0.82[EUR][1000 genomes]
rs2904222	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34115022	0.93[EUR][1000 genomes]
rs3971708	0.86[EUR][1000 genomes]
rs59709310	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3934898	CHRNA5	cis	Muscle Skeletal	GTEx
rs3934898	RP11-650L12.2	cis	Muscle Skeletal	GTEx

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

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	chr15:79043600-79077800	Weak transcription	Brain Germinal Matrix	brain
4	chr15:79044200-79059000	Enhancers	Fetal Muscle Trunk	muscle
5	chr15:79045000-79055800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:79045000-79059000	Enhancers	Fetal Muscle Leg	muscle
7	chr15:79046400-79063200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:79048200-79057000	Enhancers	Primary B cells from peripheral blood	blood
9	chr15:79049200-79058600	Enhancers	Spleen	Spleen
10	chr15:79050000-79055800	Weak transcription	Esophagus	oesophagus
11	chr15:79050000-79058600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:79050200-79056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:79051800-79070600	Weak transcription	Fetal Brain Female	brain
14	chr15:79052600-79056600	Weak transcription	Brain Substantia Nigra	brain
15	chr15:79052800-79070600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:79052800-79070800	Weak transcription	Ovary	ovary
17	chr15:79052800-79071000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:79053200-79056200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:79053200-79056400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:79053200-79063200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:79053200-79063800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:79053200-79071000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:79053600-79055800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr15:79053600-79056200	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:79053600-79056800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:79053600-79057000	Weak transcription	Brain Angular Gyrus	brain
27	chr15:79053800-79057000	Weak transcription	Brain Anterior Caudate	brain
28	chr15:79053800-79058600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:79054000-79068600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:79054000-79083200	Weak transcription	Fetal Intestine Small	intestine
31	chr15:79054200-79060000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:79054400-79070600	Weak transcription	HSMM	muscle
33	chr15:79054600-79055400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr15:79054600-79056000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:79054600-79058400	Weak transcription	Fetal Heart	heart
36	chr15:79054600-79060000	Weak transcription	HSMMtube	muscle
37	chr15:79054600-79064000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:79054600-79070000	Weak transcription	Fetal Lung	lung
39	chr15:79054600-79070400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:79054800-79070600	Weak transcription	Adipose Nuclei	Adipose
41	chr15:79055000-79055600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:79055000-79055800	Weak transcription	Right Atrium	heart
43	chr15:79055000-79056000	Weak transcription	Fetal Stomach	stomach
44	chr15:79055000-79057800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:79055000-79063000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:79055000-79069800	Weak transcription	Left Ventricle	heart
47	chr15:79055000-79076400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:79055200-79055600	Weak transcription	Primary B cells from cord blood	blood
49	chr15:79055200-79055600	Weak transcription	Lung	lung
50	chr15:79055200-79056400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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