Variant report

Variant	rs2904222
Chromosome Location	chr15:79052753-79052754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs34115022	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3934898	0.87[AMR][1000 genomes];0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2904222	CHRNA5	cis	Muscle Skeletal	GTEx

Chromatin state (count:81 , 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	chr15:79043600-79077800	Weak transcription	Brain Germinal Matrix	brain
4	chr15:79043800-79053400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:79044200-79059000	Enhancers	Fetal Muscle Trunk	muscle
6	chr15:79045000-79055800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:79045000-79059000	Enhancers	Fetal Muscle Leg	muscle
8	chr15:79046200-79054600	Enhancers	Fetal Heart	heart
9	chr15:79046400-79063200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:79047000-79053200	Enhancers	Stomach Smooth Muscle	stomach
11	chr15:79047200-79053600	Enhancers	NHDF-Ad	bronchial
12	chr15:79047200-79054600	Enhancers	HSMMtube	muscle
13	chr15:79048200-79055200	Enhancers	Primary B cells from cord blood	blood
14	chr15:79048200-79057000	Enhancers	Primary B cells from peripheral blood	blood
15	chr15:79048600-79054600	Enhancers	Placenta	Placenta
16	chr15:79048600-79055000	Enhancers	Left Ventricle	heart
17	chr15:79049200-79053400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:79049200-79055200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:79049200-79058600	Enhancers	Spleen	Spleen
20	chr15:79049400-79053400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr15:79049400-79053600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:79050000-79053000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:79050000-79053000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr15:79050000-79053000	Weak transcription	Fetal Thymus	thymus
25	chr15:79050000-79054000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:79050000-79054400	Enhancers	HSMM	muscle
27	chr15:79050000-79055800	Weak transcription	Esophagus	oesophagus
28	chr15:79050000-79058600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:79050200-79053000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:79050200-79053200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:79050200-79056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:79050400-79053000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:79050600-79053200	Enhancers	Brain Cingulate Gyrus	brain
34	chr15:79050800-79053800	Enhancers	Brain Anterior Caudate	brain
35	chr15:79051000-79052800	Enhancers	Ovary	ovary
36	chr15:79051000-79053600	Enhancers	Brain Angular Gyrus	brain
37	chr15:79051000-79053600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr15:79051000-79054800	Enhancers	Primary hematopoietic stem cells	blood
39	chr15:79051000-79054800	Enhancers	Adipose Nuclei	Adipose
40	chr15:79051200-79053600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:79051600-79052800	Enhancers	Colonic Mucosa	Colon
42	chr15:79051600-79052800	Enhancers	Pancreas	Pancrea
43	chr15:79051600-79053000	Enhancers	Rectal Smooth Muscle	rectum
44	chr15:79051600-79053200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:79051600-79053600	Enhancers	Brain Hippocampus Middle	brain
46	chr15:79051600-79054600	Enhancers	Fetal Lung	lung
47	chr15:79051600-79055000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr15:79051800-79053200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr15:79051800-79053200	Enhancers	Colon Smooth Muscle	Colon
50	chr15:79051800-79053800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links