Variant report

Variant	rs12899147
Chromosome Location	chr15:79079512-79079513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11072803	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072804	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630236	0.82[MEX][hapmap]
rs11631955	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11632102	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11634042	0.96[CEU][hapmap];0.88[CHB][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11634450	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11638321	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11639044	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11856536	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11858210	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12050525	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592721	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12903203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1809420	0.89[MEX][hapmap]
rs1825087	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1994016	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277546	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28610385	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2904220	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3825807	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886592	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4887113	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7173267	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7174367	0.84[MEX][hapmap]
rs7177699	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.92[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	nsv977739	chr15:79062099-79080757	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12899147	PSMA4	cis	parietal	SCAN
rs12899147	CHRNA5	cis	parietal	SCAN
rs12899147	CHRNA5	cis	cerebellum	SCAN
rs12899147	HMG20A	cis	parietal	SCAN
rs12899147	CLK3	cis	parietal	SCAN
rs12899147	BCL2A1	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79054000-79083200	Weak transcription	Fetal Intestine Small	intestine
2	chr15:79058000-79090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:79061000-79080000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:79061600-79080400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:79062200-79080200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:79069000-79080000	Weak transcription	Osteobl	bone
7	chr15:79069200-79090200	Weak transcription	NHDF-Ad	bronchial
8	chr15:79071200-79079800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:79071200-79080200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:79071400-79080200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:79072000-79080000	Weak transcription	NHLF	lung
12	chr15:79072000-79096600	Weak transcription	Brain Substantia Nigra	brain
13	chr15:79072000-79096800	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:79072200-79080200	Weak transcription	Lung	lung
15	chr15:79072200-79082000	Weak transcription	Right Atrium	heart
16	chr15:79072800-79080000	Weak transcription	Aorta	Aorta
17	chr15:79072800-79082000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:79072800-79089800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:79072800-79102400	Weak transcription	Fetal Kidney	kidney
20	chr15:79073800-79080200	Weak transcription	Spleen	Spleen
21	chr15:79074200-79080200	Weak transcription	Right Ventricle	heart
22	chr15:79074800-79083000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:79075600-79082200	Weak transcription	Fetal Brain Male	brain
24	chr15:79076400-79090400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:79076400-79090400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:79076400-79090800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:79077200-79080200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:79077200-79081400	Strong transcription	Fetal Lung	lung
29	chr15:79077200-79084800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:79077200-79085200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:79077200-79089800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:79077200-79096600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:79077400-79089000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:79077600-79084200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:79077600-79087800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:79077800-79080200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr15:79077800-79090600	Strong transcription	Brain Germinal Matrix	brain
38	chr15:79078000-79079600	Strong transcription	HSMM	muscle
39	chr15:79078000-79083000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:79078000-79083400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr15:79078000-79084000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:79078000-79084200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:79078000-79089400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:79078200-79093200	Strong transcription	Fetal Stomach	stomach
45	chr15:79078400-79085000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:79078400-79091800	Weak transcription	Gastric	stomach
47	chr15:79078600-79080400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr15:79078600-79080600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr15:79078600-79082000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:79078600-79083600	Strong transcription	Ovary	ovary

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