Variant report

Variant	rs7126
Chromosome Location	chr3:48485493-48485494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48485458-48485868	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:48485350-48488730	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr3:48485480-48488528	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr3:48485447-48486613	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:48485436-48488575	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:48485493-48489452	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:48485461-48485860	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:48485446-48488566	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:48485476-48485838	GM12891	blood:	n/a	n/a
10	POLR2A	chr3:48484943-48485879	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48461352..48463314-chr3:48484246..48486227,2	MCF-7	breast:
2	chr3:48485232..48487898-chr3:48541366..48542951,2	K562	blood:
3	chr3:48477555..48484761-chr3:48484855..48490000,13	MCF-7	breast:
4	chr3:48468360..48471756-chr3:48485148..48489754,5	K562	blood:
5	chr3:48484123..48488497-chr3:48591865..48597132,6	K562	blood:
6	chr3:48228273..48230987-chr3:48484727..48487110,2	K562	blood:

No data

Variant related genes	Relation type
ATRIP	TF binding region
CCDC51	TF binding region
ENSG00000164050	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000164045	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000164051	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1037773	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10470686	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1109227	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130170	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130171	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712561	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11797	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487542	0.94[EUR][1000 genomes]
rs13069724	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13071337	0.95[EUR][1000 genomes]
rs13072012	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076076	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13314659	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13324374	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459242	0.89[EUR][1000 genomes]
rs1459249	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459250	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563736	0.95[EUR][1000 genomes]
rs1824363	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1870444	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975844	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2045554	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242150	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279077	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290822	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2362450	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362452	0.89[EUR][1000 genomes]
rs28824259	0.95[EUR][1000 genomes]
rs2885509	0.90[EUR][1000 genomes]
rs2885510	0.90[EUR][1000 genomes]
rs3214041	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34761139	0.95[EUR][1000 genomes]
rs35215722	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774808	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490383	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858793	0.90[EUR][1000 genomes]
rs4858817	0.90[EUR][1000 genomes]
rs60512868	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442116	0.89[EUR][1000 genomes]
rs6442117	0.92[EUR][1000 genomes]
rs6442118	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442119	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442120	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442123	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442124	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6764415	0.86[EUR][1000 genomes]
rs6770470	0.94[EUR][1000 genomes]
rs6776700	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779262	0.90[EUR][1000 genomes]
rs6784322	0.93[EUR][1000 genomes]
rs6784541	0.93[EUR][1000 genomes]
rs6794875	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6796491	0.95[EUR][1000 genomes]
rs6800475	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804774	0.95[EUR][1000 genomes]
rs6810060	0.94[EUR][1000 genomes]
rs725309	0.90[EUR][1000 genomes]
rs725310	0.90[EUR][1000 genomes]
rs73074358	0.94[EUR][1000 genomes]
rs734072	0.81[AMR][1000 genomes]
rs7618883	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630741	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7634377	0.93[EUR][1000 genomes]
rs7635522	0.94[EUR][1000 genomes]
rs7636044	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636782	0.92[EUR][1000 genomes]
rs7639743	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653691	0.91[EUR][1000 genomes]
rs898225	0.89[EUR][1000 genomes]
rs922075	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311423	0.93[EUR][1000 genomes]
rs9311424	0.93[EUR][1000 genomes]
rs9809843	0.95[EUR][1000 genomes]
rs9812647	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9815088	0.80[AMR][1000 genomes]
rs9815103	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9817615	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9826195	0.95[EUR][1000 genomes]
rs9826247	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849509	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9862575	0.95[EUR][1000 genomes]
rs9864371	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9864815	0.95[EUR][1000 genomes]
rs9875280	0.95[EUR][1000 genomes]
rs9876781	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876891	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881491	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883759	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883927	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv965164	chr3:48485079-48485579	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7126	TMA7	cis	Muscle Skeletal	GTEx
rs7126	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs7126	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	chr3:48482600-48487200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48482600-48487200	Weak transcription	Right Atrium	heart
3	chr3:48482600-48487400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:48482600-48487600	Weak transcription	Ovary	ovary
5	chr3:48483200-48487200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:48483400-48486200	Strong transcription	Gastric	stomach
7	chr3:48483400-48486200	Strong transcription	Left Ventricle	heart
8	chr3:48483400-48486200	Strong transcription	Osteobl	bone
9	chr3:48483400-48486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48483400-48486400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:48483400-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:48483400-48486400	Strong transcription	Brain Anterior Caudate	brain
13	chr3:48483400-48486400	Strong transcription	Esophagus	oesophagus
14	chr3:48483400-48487200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:48483400-48487200	Weak transcription	Brain Angular Gyrus	brain
16	chr3:48483400-48487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:48483400-48487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:48483600-48486000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:48483600-48486200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:48483600-48486200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:48483600-48486200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:48483600-48486200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:48483600-48486200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:48483600-48486200	Strong transcription	Fetal Thymus	thymus
25	chr3:48483600-48486200	Strong transcription	Lung	lung
26	chr3:48483600-48486400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:48483600-48486400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:48483600-48486400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:48483600-48486400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:48483600-48486400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:48483600-48486400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:48483600-48486400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:48483600-48486400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:48483600-48486400	Strong transcription	Adipose Nuclei	Adipose
35	chr3:48483600-48486400	Strong transcription	Brain Hippocampus Middle	brain
36	chr3:48483600-48486400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr3:48483600-48486400	Strong transcription	Colon Smooth Muscle	Colon
38	chr3:48483600-48486400	Strong transcription	Placenta	Placenta
39	chr3:48483600-48486400	Strong transcription	Pancreas	Pancrea
40	chr3:48483600-48486400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr3:48483600-48486400	Strong transcription	NH-A	brain
42	chr3:48483600-48486600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:48483600-48486600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:48483600-48486600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:48483600-48486600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr3:48483600-48487000	Strong transcription	Brain Germinal Matrix	brain
47	chr3:48483600-48487000	Weak transcription	Fetal Heart	heart
48	chr3:48483600-48487000	Weak transcription	NHDF-Ad	bronchial
49	chr3:48483600-48487200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:48483600-48487200	Weak transcription	Fetal Brain Male	brain

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