Variant report

Variant	rs1564499
Chromosome Location	chr15:79084808-79084809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10851911	0.90[EUR][1000 genomes]
rs11630027	0.92[EUR][1000 genomes]
rs12905740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1383636	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1976007	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1994017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2046144	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28542482	0.91[EUR][1000 genomes]
rs2904228	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3743057	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs3971703	0.89[EUR][1000 genomes]
rs7183621	0.85[EUR][1000 genomes]
rs8029039	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8038189	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8042170	0.92[EUR][1000 genomes]
rs922693	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv3358739	chr15:79084409-79084954	Strong transcription Weak transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1564499	CHRNA5	cis	cerebellum	SCAN
rs1564499	HMG20A	cis	parietal	SCAN
rs1564499	BCL2A1	cis	parietal	SCAN
rs1564499	CHRNA5	cis	parietal	SCAN
rs1564499	IREB2	cis	cerebellum	SCAN
rs1564499	LMAN1L	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79058000-79090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:79069200-79090200	Weak transcription	NHDF-Ad	bronchial
3	chr15:79072000-79096600	Weak transcription	Brain Substantia Nigra	brain
4	chr15:79072000-79096800	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:79072800-79089800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr15:79072800-79102400	Weak transcription	Fetal Kidney	kidney
7	chr15:79076400-79090400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:79076400-79090400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:79076400-79090800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:79077200-79085200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:79077200-79089800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:79077200-79096600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:79077400-79089000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:79077600-79087800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:79077800-79090600	Strong transcription	Brain Germinal Matrix	brain
16	chr15:79078000-79089400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:79078200-79093200	Strong transcription	Fetal Stomach	stomach
18	chr15:79078400-79085000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:79078400-79091800	Weak transcription	Gastric	stomach
20	chr15:79078600-79085000	Strong transcription	HSMMtube	muscle
21	chr15:79078600-79089800	Weak transcription	HMEC	breast
22	chr15:79078600-79090600	Strong transcription	Fetal Brain Female	brain
23	chr15:79079000-79089600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:79079400-79091000	Weak transcription	HUVEC	blood vessel
25	chr15:79079600-79090600	Weak transcription	NH-A	brain
26	chr15:79080400-79096200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr15:79080600-79087400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:79080600-79087400	Weak transcription	Osteobl	bone
29	chr15:79080800-79089400	Weak transcription	NHLF	lung
30	chr15:79080800-79095200	Weak transcription	Fetal Intestine Large	intestine
31	chr15:79081000-79088600	Weak transcription	Placenta	Placenta
32	chr15:79082000-79088000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:79082400-79087800	Weak transcription	Lung	lung
34	chr15:79082600-79085000	Strong transcription	Right Ventricle	heart
35	chr15:79082600-79089800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:79082800-79087400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:79082800-79096200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:79082800-79102200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:79083000-79087200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:79083200-79102000	Weak transcription	Fetal Heart	heart
41	chr15:79083400-79086600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr15:79083600-79087400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:79083600-79087600	Weak transcription	Ovary	ovary
44	chr15:79083600-79089600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:79083800-79085400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:79083800-79087800	Weak transcription	Fetal Intestine Small	intestine
47	chr15:79083800-79102400	Weak transcription	Aorta	Aorta
48	chr15:79084000-79086000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:79084000-79086200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:79084000-79087400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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