Variant report

Variant	rs6442124
Chromosome Location	chr3:48505302-48505303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48504460-48507487	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:48504689-48505387	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:48504160-48505610	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr3:48504547-48505578	HL-60	blood:	n/a	n/a
5	POLR2A	chr3:48504763-48505338	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr3:48505222-48505487	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:48504839-48505418	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr3:48504333-48505403	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr3:48505220-48505370	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:48504343-48505330	GM12892	blood:	n/a	n/a
11	CTCF	chr3:48505300-48505450	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:48504169-48505907	K562	blood:	n/a	n/a
13	POLR2A	chr3:48505228-48505352	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:48504246-48505376	GM12892	blood:	n/a	n/a
15	POLR2A	chr3:48504789-48505368	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr3:48504592-48505491	K562	blood:	n/a	n/a
17	POLR2A	chr3:48504127-48505554	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr3:48504348-48505522	MCF-7	breast:	n/a	n/a
19	POLR2A	chr3:48504287-48505587	K562	blood:	n/a	n/a
20	POLR2A	chr3:48504535-48505304	U87	brain:	n/a	n/a
21	POLR2A	chr3:48504332-48505618	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:48486886..48491367-chr3:48500074..48506067,6	K562	blood:
2	chr3:48493355..48497558-chr3:48502892..48507335,5	K562	blood:
3	chr3:48504857..48507014-chr3:48585352..48587793,2	MCF-7	breast:
4	chr3:48499115..48502193-chr3:48502794..48505644,3	K562	blood:
5	chr3:48481333..48484548-chr3:48503757..48508561,5	MCF-7	breast:
6	chr3:48494179..48495965-chr3:48503697..48505795,2	K562	blood:
7	chr3:48504584..48507240-chr3:48631582..48633525,2	MCF-7	breast:
8	chr3:48485548..48495296-chr3:48503776..48510303,13	MCF-7	breast:
9	chr3:48505137..48507791-chr3:48593397..48596225,2	K562	blood:
10	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:

No data

Variant related genes	Relation type
TREX1	TF binding region
ENSG00000114270	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000114268	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1037773	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10470686	0.84[EUR][1000 genomes]
rs1109227	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130170	0.84[EUR][1000 genomes]
rs11130171	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11712561	0.83[EUR][1000 genomes]
rs11797	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12487542	0.83[EUR][1000 genomes]
rs13069724	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13071337	0.83[EUR][1000 genomes]
rs13072012	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076076	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13091785	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13314659	0.84[EUR][1000 genomes]
rs13324374	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1459249	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1459250	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1563736	0.83[EUR][1000 genomes]
rs1824363	0.95[ASN][1000 genomes]
rs1870444	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1975844	0.84[EUR][1000 genomes]
rs2045554	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242150	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279077	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290822	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2362450	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28824259	0.83[EUR][1000 genomes]
rs3214041	0.84[EUR][1000 genomes]
rs34761139	0.83[EUR][1000 genomes]
rs35215722	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3774808	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4490383	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60512868	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442117	0.81[EUR][1000 genomes]
rs6442118	0.84[EUR][1000 genomes]
rs6442119	0.84[EUR][1000 genomes]
rs6442120	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442123	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6764415	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6770470	0.83[EUR][1000 genomes]
rs6776700	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784322	0.81[EUR][1000 genomes]
rs6784541	0.81[EUR][1000 genomes]
rs6794875	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6796491	0.83[EUR][1000 genomes]
rs6800475	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804774	0.83[EUR][1000 genomes]
rs6810060	0.83[EUR][1000 genomes]
rs7126	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73074358	0.83[EUR][1000 genomes]
rs734071	0.81[AMR][1000 genomes]
rs7618883	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630741	0.80[EUR][1000 genomes]
rs7634377	0.81[EUR][1000 genomes]
rs7635522	0.83[EUR][1000 genomes]
rs7636044	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7636782	0.81[EUR][1000 genomes]
rs7639743	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs922075	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9311423	0.81[EUR][1000 genomes]
rs9311424	0.81[EUR][1000 genomes]
rs9809843	0.83[EUR][1000 genomes]
rs9812647	0.84[EUR][1000 genomes]
rs9817615	0.91[ASN][1000 genomes]
rs9826195	0.83[EUR][1000 genomes]
rs9826247	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838618	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9849509	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9862575	0.83[EUR][1000 genomes]
rs9864371	0.83[EUR][1000 genomes]
rs9864815	0.83[EUR][1000 genomes]
rs9875280	0.83[EUR][1000 genomes]
rs9876781	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876891	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9881491	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9883759	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9883927	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6442124	TMA7	cis	Muscle Skeletal	GTEx
rs6442124	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs6442124	RP11-24C3.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48489200-48506200	Weak transcription	Stomach Mucosa	stomach
2	chr3:48489200-48507400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:48489600-48506400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:48489800-48506600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:48491400-48506600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:48491800-48506400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:48492600-48505800	Strong transcription	Fetal Muscle Leg	muscle
8	chr3:48492600-48506000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:48492800-48506000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr3:48493200-48506400	Weak transcription	Fetal Heart	heart
11	chr3:48493400-48507200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:48493800-48506600	Strong transcription	Fetal Intestine Small	intestine
13	chr3:48496800-48507200	Weak transcription	Psoas Muscle	Psoas
14	chr3:48498600-48506200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:48498600-48506400	Strong transcription	Fetal Brain Female	brain
16	chr3:48499600-48505400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:48500000-48505800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr3:48500200-48506000	Strong transcription	Spleen	Spleen
19	chr3:48500800-48506600	Weak transcription	Fetal Brain Male	brain
20	chr3:48500800-48506800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:48501200-48506400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:48501200-48506400	Weak transcription	NHDF-Ad	bronchial
23	chr3:48501200-48506600	Weak transcription	Fetal Kidney	kidney
24	chr3:48501800-48506600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:48502200-48506800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:48502200-48507200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:48502400-48506800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:48502400-48507000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:48502600-48506200	Strong transcription	Placenta	Placenta
30	chr3:48502600-48506400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:48502600-48506400	Weak transcription	Brain Substantia Nigra	brain
32	chr3:48502600-48506400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:48502600-48506400	Weak transcription	Hela-S3	cervix
34	chr3:48502600-48506600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:48502600-48506600	Weak transcription	HSMM	muscle
36	chr3:48502800-48506000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:48502800-48506000	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:48502800-48506000	Weak transcription	Colonic Mucosa	Colon
39	chr3:48502800-48506000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:48502800-48506200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:48502800-48506200	Weak transcription	Gastric	stomach
42	chr3:48502800-48506200	Weak transcription	Pancreas	Pancrea
43	chr3:48502800-48506200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:48502800-48506200	Weak transcription	Right Ventricle	heart
45	chr3:48502800-48506200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:48502800-48506400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:48502800-48506400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:48502800-48506600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:48502800-48506600	Weak transcription	Primary B cells from cord blood	blood
50	chr3:48502800-48506600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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