Variant report

Variant	rs13324374
Chromosome Location	chr3:48484890-48484891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

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	chr3:48484863-48485286	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:48484059-48485410	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

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:
5	chr3:48228273..48230987-chr3:48484727..48487110,2	K562	blood:

No data

Variant related genes	Relation type
CCDC51	TF binding region
ATRIP	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000164045	Chromatin interaction
ENSG00000232112	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	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10470686	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1109227	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130170	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130171	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712561	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11797	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487542	0.94[EUR][1000 genomes]
rs13069724	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13071337	0.94[EUR][1000 genomes]
rs13072012	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076076	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091785	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13314659	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1459242	0.89[EUR][1000 genomes]
rs1459249	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459250	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563736	0.94[EUR][1000 genomes]
rs1824363	0.97[ASN][1000 genomes]
rs1870444	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975844	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2045554	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242150	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279077	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290822	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2362450	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362452	0.89[EUR][1000 genomes]
rs28824259	0.94[EUR][1000 genomes]
rs2885509	0.89[EUR][1000 genomes]
rs2885510	0.89[EUR][1000 genomes]
rs3214041	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34761139	0.94[EUR][1000 genomes]
rs35215722	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774808	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490383	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858793	0.89[EUR][1000 genomes]
rs4858817	0.89[EUR][1000 genomes]
rs60512868	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442116	0.88[EUR][1000 genomes]
rs6442117	0.91[EUR][1000 genomes]
rs6442118	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442119	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442120	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442123	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442124	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6764415	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6770470	0.94[EUR][1000 genomes]
rs6776700	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779262	0.89[EUR][1000 genomes]
rs6784322	0.92[EUR][1000 genomes]
rs6784541	0.92[EUR][1000 genomes]
rs6794875	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6796491	0.94[EUR][1000 genomes]
rs6800475	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804774	0.94[EUR][1000 genomes]
rs6810060	0.93[EUR][1000 genomes]
rs7126	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725309	0.89[EUR][1000 genomes]
rs725310	0.89[EUR][1000 genomes]
rs73074358	0.94[EUR][1000 genomes]
rs7618883	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630741	0.91[EUR][1000 genomes]
rs7634377	0.92[EUR][1000 genomes]
rs7635522	0.94[EUR][1000 genomes]
rs7636044	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636782	0.92[EUR][1000 genomes]
rs7639743	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653691	0.90[EUR][1000 genomes]
rs898225	0.89[EUR][1000 genomes]
rs922075	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311423	0.92[EUR][1000 genomes]
rs9311424	0.92[EUR][1000 genomes]
rs9809843	0.94[EUR][1000 genomes]
rs9812647	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9815103	0.90[EUR][1000 genomes]
rs9817615	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9826195	0.94[EUR][1000 genomes]
rs9826247	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838618	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849509	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9862575	0.94[EUR][1000 genomes]
rs9864371	0.94[EUR][1000 genomes]
rs9864815	0.94[EUR][1000 genomes]
rs9875280	0.94[EUR][1000 genomes]
rs9876781	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876891	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881491	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883759	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883927	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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
rs13324374	TMA7	cis	Muscle Skeletal	GTEx
rs13324374	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs13324374	TREX1	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:48483200-48487200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:48483400-48485000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:48483400-48485200	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr3:48483400-48486200	Strong transcription	Gastric	stomach
10	chr3:48483400-48486200	Strong transcription	Left Ventricle	heart
11	chr3:48483400-48486200	Strong transcription	Osteobl	bone
12	chr3:48483400-48486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:48483400-48486400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:48483400-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:48483400-48486400	Strong transcription	Brain Anterior Caudate	brain
16	chr3:48483400-48486400	Strong transcription	Esophagus	oesophagus
17	chr3:48483400-48487200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:48483400-48487200	Weak transcription	Brain Angular Gyrus	brain
19	chr3:48483400-48487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:48483400-48487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:48483600-48485000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:48483600-48485000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:48483600-48485000	Weak transcription	Brain Substantia Nigra	brain
24	chr3:48483600-48485000	Weak transcription	A549	lung
25	chr3:48483600-48485000	Enhancers	HepG2	liver
26	chr3:48483600-48485200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:48483600-48485200	Strong transcription	Fetal Lung	lung
28	chr3:48483600-48485200	Strong transcription	Right Ventricle	heart
29	chr3:48483600-48486000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:48483600-48486200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:48483600-48486200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:48483600-48486200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:48483600-48486200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:48483600-48486200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr3:48483600-48486200	Strong transcription	Fetal Thymus	thymus
36	chr3:48483600-48486200	Strong transcription	Lung	lung
37	chr3:48483600-48486400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:48483600-48486400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:48483600-48486400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:48483600-48486400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:48483600-48486400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:48483600-48486400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:48483600-48486400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:48483600-48486400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:48483600-48486400	Strong transcription	Adipose Nuclei	Adipose
46	chr3:48483600-48486400	Strong transcription	Brain Hippocampus Middle	brain
47	chr3:48483600-48486400	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr3:48483600-48486400	Strong transcription	Colon Smooth Muscle	Colon
49	chr3:48483600-48486400	Strong transcription	Placenta	Placenta
50	chr3:48483600-48486400	Strong transcription	Pancreas	Pancrea

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