Variant report

Variant	rs2005263
Chromosome Location	chr15:79032825-79032826
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	chr15:78910807..78911530-chr15:79032496..79033228,4	K562	blood:
2	chr15:78910640..78911433-chr15:79032225..79033403,4	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1045130	0.88[AMR][1000 genomes]
rs12901331	0.84[ASN][1000 genomes]
rs12906171	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1964562	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2017295	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046143	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34019568	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34067845	0.84[ASN][1000 genomes]
rs34099810	0.84[ASN][1000 genomes]
rs34422348	0.84[ASN][1000 genomes]
rs34552906	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34653907	0.81[EUR][1000 genomes]
rs34816637	0.81[AMR][1000 genomes]
rs35602248	0.83[AMR][1000 genomes]
rs35741852	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs59414039	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67775542	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][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	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2005263	CHRNA3	cis	Muscle Skeletal	GTEx
rs2005263	CHRNA5	cis	Muscle Skeletal	GTEx
rs2005263	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79031200-79033000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:79031200-79033000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:79031400-79033000	Enhancers	NHEK	skin
4	chr15:79031600-79033000	Enhancers	A549	lung
5	chr15:79031800-79033000	Enhancers	Esophagus	oesophagus
6	chr15:79031800-79033800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:79032400-79033000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:79032400-79033000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:79032400-79033000	Enhancers	Duodenum Mucosa	Duodenum
10	chr15:79032600-79033000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
11	chr15:79032600-79033000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:79032600-79033000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr15:79032600-79033000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:79032600-79033000	Enhancers	Primary B cells from peripheral blood	blood
15	chr15:79032600-79033000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr15:79032600-79033000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:79032600-79033000	Enhancers	Colonic Mucosa	Colon
18	chr15:79032600-79033000	Bivalent Enhancer	Fetal Stomach	stomach
19	chr15:79032600-79033000	Enhancers	Fetal Thymus	thymus
20	chr15:79032600-79033000	Enhancers	Pancreas	Pancrea
21	chr15:79032600-79033000	Enhancers	Psoas Muscle	Psoas
22	chr15:79032600-79033000	Enhancers	Right Ventricle	heart
23	chr15:79032600-79033000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr15:79032600-79033000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr15:79032600-79033000	Enhancers	HMEC	breast
26	chr15:79032600-79033200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr15:79032600-79033200	Enhancers	K562	blood
28	chr15:79032600-79033400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr15:79032600-79033400	Enhancers	Gastric	stomach
30	chr15:79032600-79033600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr15:79032600-79034000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr15:79032800-79033000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:79032800-79033000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
34	chr15:79032800-79033000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
35	chr15:79032800-79033000	Enhancers	Adipose Nuclei	Adipose
36	chr15:79032800-79033000	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr15:79032800-79033000	Enhancers	Hela-S3	cervix
38	chr15:79032800-79033000	Bivalent/Poised TSS	HepG2	liver
39	chr15:79032800-79033400	Enhancers	Spleen	Spleen

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