Variant report

Variant	rs8040147
Chromosome Location	chr15:59531591-59531592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs3794488	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57487429	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58579379	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59773793	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002697	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494079	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494084	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494086	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494087	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494089	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172489	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172761	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7174147	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7175876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179352	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181249	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027055	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027766	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8038705	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv904272	chr15:59500577-59549018	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv904273	chr15:59518488-59567137	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8040147	RAB27A	cis	cerebellum	SCAN
rs8040147	HSP90AB4P	cis	parietal	SCAN
rs8040147	BNIP2	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59511400-59549200	Weak transcription	Colonic Mucosa	Colon
2	chr15:59515800-59566600	Weak transcription	Pancreas	Pancrea
3	chr15:59517000-59536600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:59517600-59546400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:59517800-59564200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:59521600-59534400	Weak transcription	Placenta	Placenta
7	chr15:59521600-59566400	Weak transcription	Psoas Muscle	Psoas
8	chr15:59524000-59541800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:59524000-59542200	Weak transcription	Gastric	stomach
10	chr15:59524000-59546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:59524600-59569200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:59524600-59574600	Weak transcription	Lung	lung
13	chr15:59524800-59532800	Weak transcription	Fetal Intestine Small	intestine
14	chr15:59524800-59542200	Weak transcription	Esophagus	oesophagus
15	chr15:59525000-59531800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:59525000-59541800	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:59525000-59546400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:59525200-59532000	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:59525200-59532400	Weak transcription	Ovary	ovary
20	chr15:59525200-59532800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:59525200-59533000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:59525200-59533000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:59525200-59533200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:59525200-59540200	Weak transcription	Right Ventricle	heart
25	chr15:59525200-59543000	Weak transcription	Right Atrium	heart
26	chr15:59525200-59547800	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:59525200-59554000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:59525200-59566600	Weak transcription	Small Intestine	intestine
29	chr15:59525200-59582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:59525400-59534800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:59525400-59541000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:59525400-59542200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:59527400-59534600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:59527400-59536000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:59527600-59532800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:59528000-59533000	Weak transcription	HSMM	muscle
37	chr15:59528400-59532000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:59529200-59532000	Weak transcription	Brain Substantia Nigra	brain
39	chr15:59529200-59532000	Weak transcription	HMEC	breast
40	chr15:59529200-59532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:59529200-59534200	Weak transcription	Fetal Intestine Large	intestine
42	chr15:59529200-59535600	Weak transcription	Stomach Mucosa	stomach
43	chr15:59529200-59540800	Weak transcription	Adipose Nuclei	Adipose
44	chr15:59529200-59547200	Weak transcription	Aorta	Aorta
45	chr15:59529200-59547800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:59529600-59532800	Weak transcription	HSMMtube	muscle
47	chr15:59529600-59535600	Weak transcription	NH-A	brain
48	chr15:59529800-59539800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:59529800-59545000	Weak transcription	HepG2	liver
50	chr15:59530000-59532600	Weak transcription	Muscle Satellite Cultured Cells	--

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