Variant report

Variant	rs8080334
Chromosome Location	chr17:17954764-17954765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:17954711-17954989	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17954468..17957000-chr17:18063642..18065994,2	MCF-7	breast:

Variant related genes	Relation type
GID4	TF binding region
ENSG00000091536	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11078408	0.84[ASN][1000 genomes]
rs11650021	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11658257	0.84[ASN][1000 genomes]
rs12150369	0.82[AMR][1000 genomes]
rs12939020	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12940282	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28537385	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2955350	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2955352	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2955353	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2955354	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2955355	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2955356	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2955357	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2955358	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2955359	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2955369	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2955370	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2955372	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2955377	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2955378	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2955380	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2955381	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2955383	0.86[AMR][1000 genomes]
rs2955384	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2955385	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3935505	0.84[ASN][1000 genomes]
rs3935506	0.84[ASN][1000 genomes]
rs4365348	0.82[AMR][1000 genomes]
rs4368210	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4506969	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4584886	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4643387	0.86[AMR][1000 genomes]
rs4925135	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925136	0.87[AMR][1000 genomes]
rs62072050	0.85[AMR][1000 genomes]
rs6502632	0.85[AMR][1000 genomes]
rs6502633	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6502634	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7207461	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7207821	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7209003	0.81[AMR][1000 genomes]
rs7210400	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7212167	0.84[AMR][1000 genomes]
rs7215524	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7223696	0.82[AMR][1000 genomes]
rs7224047	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7406982	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7503738	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8069811	0.82[AMR][1000 genomes]
rs8070731	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8071238	0.84[ASN][1000 genomes]
rs8080602	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8082590	0.87[AMR][1000 genomes]
rs9894138	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9896837	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9897761	0.82[AMR][1000 genomes]
rs9914127	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8080334	SREBF1	cis	Whole Blood	GTEx
rs8080334	PEMT	cis	Whole Blood	GTEx

Chromatin state (count:124 , 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	chr17:17944200-17956000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr17:17944200-17957200	Weak transcription	NH-A	brain
5	chr17:17944200-17957400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr17:17944200-17957400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr17:17944200-17974400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:17944400-17957200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr17:17944400-17957200	Weak transcription	Gastric	stomach
10	chr17:17944400-17957200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr17:17944400-17957600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr17:17944400-17961800	Weak transcription	Fetal Kidney	kidney
13	chr17:17944400-17962000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr17:17944400-17978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:17944600-17957200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr17:17945000-17957000	Weak transcription	Fetal Lung	lung
17	chr17:17945000-17957400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr17:17945000-17960000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr17:17945200-17965200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr17:17945400-17955400	Weak transcription	HSMMtube	muscle
21	chr17:17945400-17957200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr17:17945400-17957600	Weak transcription	Pancreas	Pancrea
23	chr17:17945400-17957600	Weak transcription	GM12878-XiMat	blood
24	chr17:17945400-17959600	Weak transcription	Esophagus	oesophagus
25	chr17:17945400-17959800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr17:17945400-17967200	Weak transcription	Small Intestine	intestine
27	chr17:17945800-17957200	Weak transcription	HMEC	breast
28	chr17:17945800-17957600	Weak transcription	Brain Hippocampus Middle	brain
29	chr17:17945800-17957600	Weak transcription	NHLF	lung
30	chr17:17946000-17956800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr17:17946000-17957600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr17:17946800-17957400	Weak transcription	HUVEC	blood vessel
33	chr17:17947000-17957200	Weak transcription	NHDF-Ad	bronchial
34	chr17:17947000-17974400	Weak transcription	Fetal Heart	heart
35	chr17:17947400-17959600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:17947400-17963400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr17:17948600-17957600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr17:17948600-17964400	Weak transcription	K562	blood
39	chr17:17949200-17957400	Weak transcription	Colon Smooth Muscle	Colon
40	chr17:17949600-17959600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:17949800-17957000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr17:17949800-17957200	Weak transcription	Primary B cells from cord blood	blood
43	chr17:17950000-17955600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr17:17950000-17974400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr17:17950800-17955600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:17950800-17974000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr17:17951000-17955400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:17951000-17955400	Weak transcription	NHEK	skin
49	chr17:17951000-17955600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr17:17951000-17955800	Weak transcription	Stomach Smooth Muscle	stomach

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