Variant report

Variant	rs12939020
Chromosome Location	chr17:17950163-17950164
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	chr17:17943291..17945183-chr17:17948425..17950238,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1008135	0.81[EUR][1000 genomes]
rs1101727	0.81[EUR][1000 genomes]
rs11650021	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869491	0.83[EUR][1000 genomes]
rs11870660	0.85[ASN][1000 genomes]
rs11871231	0.84[EUR][1000 genomes]
rs12150369	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12940282	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12948749	0.82[EUR][1000 genomes]
rs28537385	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28555361	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2955350	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2955352	0.84[AMR][1000 genomes]
rs2955353	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2955354	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2955355	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955356	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955357	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955358	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955359	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2955365	0.81[EUR][1000 genomes]
rs2955366	0.81[EUR][1000 genomes]
rs2955368	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2955369	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2955370	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2955371	0.81[EUR][1000 genomes]
rs2955372	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2955377	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2955378	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2955380	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2955381	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2955383	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955384	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2955385	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2974998	0.83[EUR][1000 genomes]
rs2974999	0.82[EUR][1000 genomes]
rs4072738	0.84[EUR][1000 genomes]
rs4072739	0.84[EUR][1000 genomes]
rs4299203	0.83[ASN][1000 genomes]
rs4365346	0.82[EUR][1000 genomes]
rs4365348	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4368210	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4410135	0.84[EUR][1000 genomes]
rs4426402	0.83[EUR][1000 genomes]
rs4459604	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4506969	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4561528	0.82[EUR][1000 genomes]
rs4584886	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4643387	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924832	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925135	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925136	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57728924	0.83[ASN][1000 genomes]
rs59304093	0.81[ASN][1000 genomes]
rs59518074	0.84[EUR][1000 genomes]
rs62072048	0.80[EUR][1000 genomes]
rs62072050	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62073573	0.84[EUR][1000 genomes]
rs6502631	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502632	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502633	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6502634	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6502636	0.83[EUR][1000 genomes]
rs6502637	0.82[EUR][1000 genomes]
rs6826	0.81[EUR][1000 genomes]
rs712267	0.81[EUR][1000 genomes]
rs712268	0.81[EUR][1000 genomes]
rs7207461	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7207821	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7209003	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7210400	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211714	0.83[EUR][1000 genomes]
rs7212167	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212447	0.82[EUR][1000 genomes]
rs7215524	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs721669	0.81[EUR][1000 genomes]
rs7219320	0.81[ASN][1000 genomes]
rs7219324	0.85[EUR][1000 genomes]
rs7223696	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7224047	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7406744	0.82[EUR][1000 genomes]
rs7406982	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs741782	0.81[EUR][1000 genomes]
rs7503738	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8066764	0.82[EUR][1000 genomes]
rs8068175	0.85[ASN][1000 genomes]
rs8069811	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070731	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8071238	0.81[EUR][1000 genomes]
rs8075189	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080334	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8080602	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8082590	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs854763	0.81[EUR][1000 genomes]
rs854767	0.81[EUR][1000 genomes]
rs854768	0.81[EUR][1000 genomes]
rs854769	0.81[EUR][1000 genomes]
rs854770	0.81[EUR][1000 genomes]
rs854789	0.81[EUR][1000 genomes]
rs854791	0.80[EUR][1000 genomes]
rs854808	0.81[EUR][1000 genomes]
rs854809	0.81[EUR][1000 genomes]
rs854814	0.80[EUR][1000 genomes]
rs854817	0.81[EUR][1000 genomes]
rs9303144	0.82[EUR][1000 genomes]
rs9894138	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9896837	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9897761	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899355	0.84[EUR][1000 genomes]
rs9911850	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9912096	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913277	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12939020	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:123 , 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	chr17:17944200-17950400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr17:17944200-17956000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:17944200-17957200	Weak transcription	NH-A	brain
6	chr17:17944200-17957400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:17944200-17957400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr17:17944200-17974400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:17944400-17950600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr17:17944400-17957200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr17:17944400-17957200	Weak transcription	Gastric	stomach
12	chr17:17944400-17957200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr17:17944400-17957600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr17:17944400-17961800	Weak transcription	Fetal Kidney	kidney
15	chr17:17944400-17962000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr17:17944400-17978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:17944600-17957200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:17944800-17950200	Weak transcription	A549	lung
19	chr17:17944800-17950400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr17:17945000-17957000	Weak transcription	Fetal Lung	lung
21	chr17:17945000-17957400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:17945000-17960000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr17:17945200-17950400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr17:17945200-17953400	Weak transcription	Brain Anterior Caudate	brain
25	chr17:17945200-17965200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr17:17945400-17955400	Weak transcription	HSMMtube	muscle
27	chr17:17945400-17957200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr17:17945400-17957600	Weak transcription	Pancreas	Pancrea
29	chr17:17945400-17957600	Weak transcription	GM12878-XiMat	blood
30	chr17:17945400-17959600	Weak transcription	Esophagus	oesophagus
31	chr17:17945400-17959800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr17:17945400-17967200	Weak transcription	Small Intestine	intestine
33	chr17:17945800-17950200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr17:17945800-17950200	Weak transcription	Hela-S3	cervix
35	chr17:17945800-17950400	Weak transcription	HSMM	muscle
36	chr17:17945800-17957200	Weak transcription	HMEC	breast
37	chr17:17945800-17957600	Weak transcription	Brain Hippocampus Middle	brain
38	chr17:17945800-17957600	Weak transcription	NHLF	lung
39	chr17:17946000-17956800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr17:17946000-17957600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr17:17946400-17951000	Strong transcription	Fetal Muscle Leg	muscle
42	chr17:17946400-17951200	Strong transcription	Dnd41	blood
43	chr17:17946600-17950200	Weak transcription	Fetal Brain Female	brain
44	chr17:17946600-17953200	Weak transcription	Fetal Brain Male	brain
45	chr17:17946600-17954400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:17946800-17957400	Weak transcription	HUVEC	blood vessel
47	chr17:17947000-17957200	Weak transcription	NHDF-Ad	bronchial
48	chr17:17947000-17974400	Weak transcription	Fetal Heart	heart
49	chr17:17947400-17950800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:17947400-17951000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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