Variant report

Variant	rs4553680
Chromosome Location	chr17:17857722-17857723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17857581..17859340-chr17:18085372..18086963,2	K562	blood:
2	chr17:17852683..17854657-chr17:17857266..17858926,2	K562	blood:
3	chr17:17855039..17859683-chr17:17860221..17864104,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091542	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10048206	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11078400	0.80[EUR][1000 genomes]
rs11078403	0.90[EUR][1000 genomes]
rs11078404	0.95[EUR][1000 genomes]
rs11078405	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078406	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11078407	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11078408	0.82[EUR][1000 genomes]
rs11650649	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11650890	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11656840	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11657074	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11657773	0.86[EUR][1000 genomes]
rs11657845	0.87[EUR][1000 genomes]
rs11869536	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11870660	0.82[EUR][1000 genomes]
rs11871899	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452219	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452254	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600546	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12603148	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12936037	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12941039	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12943500	0.91[ASN][1000 genomes]
rs1889014	0.91[ASN][1000 genomes]
rs2350977	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28428991	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4077198	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4077828	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4244602	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257260	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4299203	0.82[EUR][1000 genomes]
rs4321247	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4341796	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343339	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4413022	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4414547	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4470201	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4471742	0.82[EUR][1000 genomes]
rs4534911	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616340	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4925123	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925125	0.90[EUR][1000 genomes]
rs4925126	0.92[EUR][1000 genomes]
rs4925129	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925130	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002487	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57728924	0.82[EUR][1000 genomes]
rs62064156	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62064158	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62072049	0.86[EUR][1000 genomes]
rs6502619	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502622	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6502624	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6502625	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502626	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502627	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502629	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66531105	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67253360	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7207043	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7207395	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208190	0.93[EUR][1000 genomes]
rs7213225	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7214002	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7214536	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7219320	0.82[EUR][1000 genomes]
rs7222480	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224815	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7503334	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065416	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8065497	0.91[ASN][1000 genomes]
rs8065563	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065970	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8066982	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8068175	0.82[EUR][1000 genomes]
rs8068820	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8070128	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8070624	0.95[ASN][1000 genomes]
rs8070722	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8070748	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8073001	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8075965	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8076747	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8077338	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077530	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8078105	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8078138	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078583	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080823	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950966	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9635697	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9635698	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9890341	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9895750	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9904163	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9905284	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9907246	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9908299	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9908832	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9912895	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9913724	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9914127	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
rs4553680	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17828200-17861000	Weak transcription	Primary B cells from cord blood	blood
2	chr17:17828600-17858000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr17:17839400-17858800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:17839400-17860200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr17:17839800-17859800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr17:17844800-17859800	Weak transcription	Colonic Mucosa	Colon
7	chr17:17844800-17861400	Weak transcription	Liver	Liver
8	chr17:17847000-17858000	Weak transcription	Adipose Nuclei	Adipose
9	chr17:17847000-17860200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr17:17847200-17861400	Weak transcription	Fetal Kidney	kidney
11	chr17:17847400-17859800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:17847400-17860200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:17847400-17860600	Weak transcription	K562	blood
14	chr17:17847400-17861600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr17:17847400-17864000	Weak transcription	Aorta	Aorta
16	chr17:17847600-17860200	Weak transcription	Hela-S3	cervix
17	chr17:17848400-17858000	Weak transcription	Brain Hippocampus Middle	brain
18	chr17:17848400-17859800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:17848400-17861200	Weak transcription	Fetal Muscle Leg	muscle
20	chr17:17848400-17862200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr17:17848600-17858000	Weak transcription	HSMMtube	muscle
22	chr17:17848600-17860600	Weak transcription	Colon Smooth Muscle	Colon
23	chr17:17848600-17861400	Weak transcription	Brain Substantia Nigra	brain
24	chr17:17848600-17861600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr17:17848800-17858000	Weak transcription	Fetal Heart	heart
26	chr17:17848800-17863000	Weak transcription	Fetal Brain Female	brain
27	chr17:17849000-17861600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr17:17849600-17858000	Weak transcription	Fetal Intestine Large	intestine
29	chr17:17849600-17858200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr17:17849600-17860400	Weak transcription	Small Intestine	intestine
31	chr17:17849800-17858000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr17:17850800-17860200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr17:17851000-17859800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr17:17851000-17860200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr17:17851800-17858400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr17:17851800-17860400	Weak transcription	HUVEC	blood vessel
37	chr17:17851800-17860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr17:17851800-17860600	Weak transcription	NH-A	brain
39	chr17:17852000-17858400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr17:17852400-17858000	Weak transcription	Fetal Intestine Small	intestine
41	chr17:17852400-17858200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr17:17852400-17860600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:17852600-17859800	Weak transcription	Stomach Mucosa	stomach
44	chr17:17852800-17858200	Weak transcription	NHLF	lung
45	chr17:17852800-17860400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr17:17852800-17862000	Weak transcription	Pancreas	Pancrea
47	chr17:17853000-17859800	Weak transcription	Gastric	stomach
48	chr17:17853000-17861600	Weak transcription	Brain Angular Gyrus	brain
49	chr17:17853200-17859800	Weak transcription	Lung	lung
50	chr17:17854400-17858400	Weak transcription	Esophagus	oesophagus

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