Variant report

Variant	rs8082590
Chromosome Location	chr17:17958402-17958403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17940893..17944721-chr17:17958076..17961039,3	K562	blood:

Variant related genes	Relation type
ENSG00000141034	Chromatin interaction
ENSG00000171953	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11650021	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11652894	0.81[EUR][1000 genomes]
rs11870660	0.85[ASN][1000 genomes]
rs11871231	0.81[EUR][1000 genomes]
rs12150369	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12939020	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12940282	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28537385	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28555361	0.84[AMR][1000 genomes]
rs2955350	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955352	0.81[AMR][1000 genomes]
rs2955353	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955354	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955355	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2955356	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2955357	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2955358	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2955359	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955368	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2955369	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955370	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955372	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2955377	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2955378	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2955380	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2955381	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2955383	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2955384	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2955385	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4072738	0.81[EUR][1000 genomes]
rs4072739	0.81[EUR][1000 genomes]
rs4299203	0.83[ASN][1000 genomes]
rs4365348	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4368210	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4410135	0.81[EUR][1000 genomes]
rs4426402	0.82[EUR][1000 genomes]
rs4459604	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4506969	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4584886	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4643387	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924832	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4925135	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4925136	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57728924	0.83[ASN][1000 genomes]
rs59304093	0.81[ASN][1000 genomes]
rs59518074	0.81[EUR][1000 genomes]
rs62072050	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62073573	0.81[EUR][1000 genomes]
rs6502631	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6502632	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6502633	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6502634	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7207461	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7207821	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7209003	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7210400	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7212167	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7215524	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7219320	0.81[ASN][1000 genomes]
rs7219324	0.81[EUR][1000 genomes]
rs7223696	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7224047	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7406982	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7503738	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8068175	0.85[ASN][1000 genomes]
rs8069811	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8070731	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8075189	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080334	0.87[AMR][1000 genomes]
rs8080602	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9894138	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9896837	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9897761	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9899355	0.80[EUR][1000 genomes]
rs9911850	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9912096	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9913277	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking 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 miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	25056061	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8082590	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17944000-17974200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:17944000-17974200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:17944200-17974400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:17944400-17961800	Weak transcription	Fetal Kidney	kidney
5	chr17:17944400-17962000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr17:17944400-17978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:17945000-17960000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:17945200-17965200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:17945400-17959600	Weak transcription	Esophagus	oesophagus
10	chr17:17945400-17959800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:17945400-17967200	Weak transcription	Small Intestine	intestine
12	chr17:17947000-17974400	Weak transcription	Fetal Heart	heart
13	chr17:17947400-17959600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr17:17947400-17963400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:17948600-17964400	Weak transcription	K562	blood
16	chr17:17949600-17959600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:17950000-17974400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:17950800-17974000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr17:17951000-17959600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:17951000-17962000	Weak transcription	Colonic Mucosa	Colon
21	chr17:17951000-17965600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr17:17952600-17960600	Strong transcription	Fetal Thymus	thymus
23	chr17:17952800-17959200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr17:17953000-17960400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:17953400-17970000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:17953600-17966000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:17954000-17959600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:17954000-17968600	Weak transcription	Psoas Muscle	Psoas
29	chr17:17954200-17974200	Weak transcription	Fetal Brain Male	brain
30	chr17:17954800-17974200	Weak transcription	Stomach Mucosa	stomach
31	chr17:17955200-17963000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:17955400-17959600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:17955400-17960600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr17:17955600-17958600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:17955600-17960400	Strong transcription	A549	lung
36	chr17:17955600-17960600	Strong transcription	Fetal Intestine Large	intestine
37	chr17:17955600-17960600	Strong transcription	Fetal Stomach	stomach
38	chr17:17955600-17960600	Strong transcription	Thymus	Thymus
39	chr17:17955600-17963200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr17:17955600-17963200	Strong transcription	Dnd41	blood
41	chr17:17955600-17969400	Strong transcription	Fetal Muscle Leg	muscle
42	chr17:17955600-17969800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr17:17955600-17970600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr17:17955600-17971200	Strong transcription	Liver	Liver
45	chr17:17956600-17960200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:17956600-17960600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr17:17956600-17970800	Strong transcription	Fetal Intestine Small	intestine
48	chr17:17956800-17958600	Strong transcription	Spleen	Spleen
49	chr17:17956800-17960200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr17:17956800-17960400	Strong transcription	Placenta	Placenta

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