Variant report

Variant	rs62072048
Chromosome Location	chr17:17894750-17894751
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	FOSL1	chr17:17894212-17894789	HCT-116	colon:	n/a	chr17:17894517-17894529
2	FOS	chr17:17894258-17894751	MCF10A-Er-Src	breast:	n/a	chr17:17894517-17894529
3	SP1	chr17:17894129-17894754	A549	lung:	n/a	n/a
4	SP1	chr17:17894100-17894766	A549	lung:	n/a	n/a

Variant related genes	Relation type
LRRC48	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11078408	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11078409	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11650021	0.82[EUR][1000 genomes]
rs11869491	0.86[EUR][1000 genomes]
rs11870660	0.82[EUR][1000 genomes]
rs11871231	0.87[EUR][1000 genomes]
rs12150369	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12603148	0.81[AFR][1000 genomes]
rs12939020	0.80[EUR][1000 genomes]
rs12940282	0.80[AMR][1000 genomes]
rs28537385	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955350	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955353	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955354	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955355	0.83[EUR][1000 genomes]
rs2955356	0.83[EUR][1000 genomes]
rs2955357	0.83[EUR][1000 genomes]
rs2955358	0.83[EUR][1000 genomes]
rs2955359	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955368	0.82[EUR][1000 genomes]
rs2955370	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955372	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2955377	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2955378	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2955380	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955381	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2955383	0.85[EUR][1000 genomes]
rs2955384	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2955385	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4072738	0.87[EUR][1000 genomes]
rs4072739	0.87[EUR][1000 genomes]
rs4299203	0.82[EUR][1000 genomes]
rs4365348	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4368210	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4459604	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4471742	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4506969	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4584886	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4635395	0.81[AFR][1000 genomes]
rs4643387	0.80[EUR][1000 genomes]
rs4924832	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4925135	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4925136	0.83[EUR][1000 genomes]
rs57728924	0.82[EUR][1000 genomes]
rs62072050	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6502631	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6502632	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6502633	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7207461	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7207821	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7209003	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7210400	0.83[EUR][1000 genomes]
rs7212167	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7215524	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7219320	0.81[EUR][1000 genomes]
rs7219324	0.85[EUR][1000 genomes]
rs7223696	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7224047	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7406982	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7503738	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8068175	0.82[EUR][1000 genomes]
rs8069811	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8071238	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8075189	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8080602	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9894138	0.83[EUR][1000 genomes]
rs9896837	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9897761	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9899355	0.86[EUR][1000 genomes]
rs9911850	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9912096	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9913277	0.89[EUR][1000 genomes]
rs9914127	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][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
rs62072048	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876400-17903200	Weak transcription	Gastric	stomach
2	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
3	chr17:17876800-17909400	Weak transcription	Brain Substantia Nigra	brain
4	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
5	chr17:17877000-17900000	Weak transcription	Fetal Intestine Small	intestine
6	chr17:17881800-17908200	Weak transcription	Pancreas	Pancrea
7	chr17:17884600-17897400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr17:17886800-17909400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr17:17886800-17913000	Weak transcription	Fetal Lung	lung
10	chr17:17887200-17900800	Weak transcription	Left Ventricle	heart
11	chr17:17888400-17897800	Weak transcription	Fetal Brain Female	brain
12	chr17:17889000-17907400	Weak transcription	Brain Anterior Caudate	brain
13	chr17:17889400-17897800	Weak transcription	Right Ventricle	heart
14	chr17:17890000-17907400	Weak transcription	Brain Germinal Matrix	brain
15	chr17:17892200-17908400	Weak transcription	Lung	lung
16	chr17:17892400-17897600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr17:17892400-17910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:17892600-17895800	Weak transcription	Fetal Stomach	stomach
19	chr17:17892600-17897400	Weak transcription	Brain Hippocampus Middle	brain
20	chr17:17892600-17897800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:17892600-17909800	Weak transcription	Brain Angular Gyrus	brain
22	chr17:17892800-17895000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr17:17892800-17908000	Weak transcription	Spleen	Spleen
24	chr17:17893000-17897600	Weak transcription	Ovary	ovary
25	chr17:17893200-17895000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:17893200-17895200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:17893200-17895200	Enhancers	NH-A	brain
28	chr17:17893200-17895200	Enhancers	NHEK	skin
29	chr17:17893400-17895200	Enhancers	HMEC	breast
30	chr17:17893600-17895000	Enhancers	NHDF-Ad	bronchial
31	chr17:17893600-17895200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr17:17893600-17897000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:17893600-17900000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr17:17893800-17895000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr17:17893800-17897000	Weak transcription	Esophagus	oesophagus
36	chr17:17893800-17897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr17:17893800-17897800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr17:17893800-17898000	Weak transcription	Right Atrium	heart
39	chr17:17894000-17895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr17:17894000-17895200	Enhancers	Hela-S3	cervix
41	chr17:17894000-17895400	Enhancers	A549	lung
42	chr17:17894000-17896200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr17:17894000-17896400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr17:17894000-17896800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr17:17894000-17897000	Weak transcription	Fetal Muscle Leg	muscle
46	chr17:17894000-17897000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr17:17894000-17903400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr17:17894000-17920600	Weak transcription	Stomach Mucosa	stomach
49	chr17:17894200-17896800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:17894200-17898000	Weak transcription	HSMM	muscle

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