Variant report

Variant	rs4490383
Chromosome Location	chr3:48484683-48484684
allele	C/T
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	chr3:48484670-48485413	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:48484426-48484961	K562	blood:	n/a	n/a
3	POLR2A	chr3:48484036-48485400	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:48484116-48484781	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:48484198-48484820	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr3:48484059-48485410	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48461352..48463314-chr3:48484246..48486227,2	MCF-7	breast:
2	chr3:48477555..48484761-chr3:48484855..48490000,13	MCF-7	breast:
3	chr3:48472201..48473721-chr3:48483082..48485224,2	MCF-7	breast:
4	chr3:48484123..48488497-chr3:48591865..48597132,6	K562	blood:

Variant related genes	Relation type
ATRIP	TF binding region
CCDC51	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000164053	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1037773	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10470686	0.93[EUR][1000 genomes]
rs1109227	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130170	0.93[EUR][1000 genomes]
rs11130171	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11712561	0.91[EUR][1000 genomes]
rs11797	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12487542	0.91[EUR][1000 genomes]
rs13069724	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13071337	0.92[EUR][1000 genomes]
rs13072012	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13076076	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13091785	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13314659	0.93[EUR][1000 genomes]
rs13324374	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1459242	0.88[EUR][1000 genomes]
rs1459249	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1459250	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1563736	0.92[EUR][1000 genomes]
rs1824363	0.92[ASN][1000 genomes]
rs1870444	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1975844	0.92[EUR][1000 genomes]
rs2045554	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242150	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2279077	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290822	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2362450	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2362452	0.86[EUR][1000 genomes]
rs28824259	0.92[EUR][1000 genomes]
rs2885509	0.87[EUR][1000 genomes]
rs2885510	0.87[EUR][1000 genomes]
rs3214041	0.93[EUR][1000 genomes]
rs34761139	0.92[EUR][1000 genomes]
rs35215722	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774808	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858793	0.87[EUR][1000 genomes]
rs4858817	0.87[EUR][1000 genomes]
rs60512868	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6442116	0.86[EUR][1000 genomes]
rs6442117	0.89[EUR][1000 genomes]
rs6442118	0.93[EUR][1000 genomes]
rs6442119	0.93[EUR][1000 genomes]
rs6442120	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442123	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442124	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6764415	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6770470	0.91[EUR][1000 genomes]
rs6776700	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6779262	0.87[EUR][1000 genomes]
rs6784322	0.90[EUR][1000 genomes]
rs6784541	0.90[EUR][1000 genomes]
rs6794875	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6796491	0.92[EUR][1000 genomes]
rs6800475	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6804774	0.92[EUR][1000 genomes]
rs6810060	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7126	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs725309	0.87[EUR][1000 genomes]
rs725310	0.87[EUR][1000 genomes]
rs73074358	0.91[EUR][1000 genomes]
rs7618883	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7630741	0.88[EUR][1000 genomes]
rs7634377	0.90[EUR][1000 genomes]
rs7635522	0.91[EUR][1000 genomes]
rs7636044	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7636782	0.89[EUR][1000 genomes]
rs7639743	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7653691	0.88[EUR][1000 genomes]
rs898225	0.88[EUR][1000 genomes]
rs922075	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9311423	0.90[EUR][1000 genomes]
rs9311424	0.90[EUR][1000 genomes]
rs9809843	0.92[EUR][1000 genomes]
rs9812647	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9815103	0.88[EUR][1000 genomes]
rs9817615	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9826195	0.92[EUR][1000 genomes]
rs9826247	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9838618	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9849509	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9862575	0.92[EUR][1000 genomes]
rs9864371	0.92[EUR][1000 genomes]
rs9864815	0.92[EUR][1000 genomes]
rs9875280	0.92[EUR][1000 genomes]
rs9876781	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876891	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9881491	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9883759	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9883927	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4490383	TMA7	cis	Muscle Skeletal	GTEx
rs4490383	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs4490383	RP11-24C3.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48482400-48485000	Weak transcription	Aorta	Aorta
2	chr3:48482600-48487200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:48482600-48487200	Weak transcription	Right Atrium	heart
4	chr3:48482600-48487400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:48482600-48487600	Weak transcription	Ovary	ovary
6	chr3:48483000-48484800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
7	chr3:48483200-48487200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:48483400-48484800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:48483400-48485000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:48483400-48485200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr3:48483400-48486200	Strong transcription	Gastric	stomach
12	chr3:48483400-48486200	Strong transcription	Left Ventricle	heart
13	chr3:48483400-48486200	Strong transcription	Osteobl	bone
14	chr3:48483400-48486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:48483400-48486400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:48483400-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:48483400-48486400	Strong transcription	Brain Anterior Caudate	brain
18	chr3:48483400-48486400	Strong transcription	Esophagus	oesophagus
19	chr3:48483400-48487200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:48483400-48487200	Weak transcription	Brain Angular Gyrus	brain
21	chr3:48483400-48487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:48483400-48487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:48483600-48484800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:48483600-48485000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:48483600-48485000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:48483600-48485000	Weak transcription	Brain Substantia Nigra	brain
27	chr3:48483600-48485000	Weak transcription	A549	lung
28	chr3:48483600-48485000	Enhancers	HepG2	liver
29	chr3:48483600-48485200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:48483600-48485200	Strong transcription	Fetal Lung	lung
31	chr3:48483600-48485200	Strong transcription	Right Ventricle	heart
32	chr3:48483600-48486000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:48483600-48486200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:48483600-48486200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:48483600-48486200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:48483600-48486200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:48483600-48486200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:48483600-48486200	Strong transcription	Fetal Thymus	thymus
39	chr3:48483600-48486200	Strong transcription	Lung	lung
40	chr3:48483600-48486400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:48483600-48486400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:48483600-48486400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:48483600-48486400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:48483600-48486400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:48483600-48486400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:48483600-48486400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:48483600-48486400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:48483600-48486400	Strong transcription	Adipose Nuclei	Adipose
49	chr3:48483600-48486400	Strong transcription	Brain Hippocampus Middle	brain
50	chr3:48483600-48486400	Strong transcription	Brain Inferior Temporal Lobe	brain

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