Variant report

Variant	rs35215722
Chromosome Location	chr3:48484021-48484022
allele	C/G/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	chr3:48483444-48484155	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48481333..48484548-chr3:48503757..48508561,5	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:

Variant related genes	Relation type
CCDC51	TF binding region
ATRIP	TF binding region
ENSG00000213689	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];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10470686	0.92[EUR][1000 genomes]
rs1109227	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130170	0.92[EUR][1000 genomes]
rs11130171	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11712561	0.90[EUR][1000 genomes]
rs11797	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12487542	0.90[EUR][1000 genomes]
rs13069724	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13071337	0.91[EUR][1000 genomes]
rs13072012	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13076076	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13091785	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13314659	0.92[EUR][1000 genomes]
rs13324374	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459242	0.85[EUR][1000 genomes]
rs1459249	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459250	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1563736	0.91[EUR][1000 genomes]
rs1824363	0.88[ASN][1000 genomes]
rs1870444	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1975844	0.91[EUR][1000 genomes]
rs2045554	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2242150	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2279077	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290822	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2362450	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2362452	0.85[EUR][1000 genomes]
rs28824259	0.91[EUR][1000 genomes]
rs2885509	0.86[EUR][1000 genomes]
rs2885510	0.86[EUR][1000 genomes]
rs3214041	0.92[EUR][1000 genomes]
rs34761139	0.91[EUR][1000 genomes]
rs3774808	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4490383	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858793	0.86[EUR][1000 genomes]
rs4858817	0.86[EUR][1000 genomes]
rs60512868	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6442116	0.85[EUR][1000 genomes]
rs6442117	0.88[EUR][1000 genomes]
rs6442118	0.92[EUR][1000 genomes]
rs6442119	0.92[EUR][1000 genomes]
rs6442120	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6442123	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6442124	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6764415	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6770470	0.90[EUR][1000 genomes]
rs6776700	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6779262	0.86[EUR][1000 genomes]
rs6784322	0.89[EUR][1000 genomes]
rs6784541	0.89[EUR][1000 genomes]
rs6794875	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6796491	0.91[EUR][1000 genomes]
rs6800475	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804774	0.91[EUR][1000 genomes]
rs6810060	0.90[EUR][1000 genomes]
rs7126	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs725309	0.86[EUR][1000 genomes]
rs725310	0.86[EUR][1000 genomes]
rs73074358	0.90[EUR][1000 genomes]
rs7618883	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7630741	0.87[EUR][1000 genomes]
rs7634377	0.89[EUR][1000 genomes]
rs7635522	0.90[EUR][1000 genomes]
rs7636044	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7636782	0.88[EUR][1000 genomes]
rs7639743	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7653691	0.87[EUR][1000 genomes]
rs898225	0.85[EUR][1000 genomes]
rs922075	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311423	0.89[EUR][1000 genomes]
rs9311424	0.89[EUR][1000 genomes]
rs9809843	0.91[EUR][1000 genomes]
rs9812647	0.92[EUR][1000 genomes]
rs9815103	0.87[EUR][1000 genomes]
rs9817615	0.87[ASN][1000 genomes]
rs9826195	0.91[EUR][1000 genomes]
rs9826247	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9838618	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9849509	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9862575	0.91[EUR][1000 genomes]
rs9864371	0.91[EUR][1000 genomes]
rs9864815	0.91[EUR][1000 genomes]
rs9875280	0.91[EUR][1000 genomes]
rs9876781	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9876891	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9881491	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9883759	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9883927	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[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
rs35215722	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs35215722	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs35215722	TMA7	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	chr3:48482800-48484400	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr3:48482800-48484400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr3:48483000-48484400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:48483000-48484400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
10	chr3:48483000-48484800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
11	chr3:48483200-48484200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:48483200-48484200	Genic enhancers	Fetal Intestine Large	intestine
13	chr3:48483200-48484600	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr3:48483200-48487200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:48483400-48484200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:48483400-48484400	Strong transcription	K562	blood
17	chr3:48483400-48484600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:48483400-48484800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:48483400-48485000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:48483400-48485200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr3:48483400-48486200	Strong transcription	Gastric	stomach
22	chr3:48483400-48486200	Strong transcription	Left Ventricle	heart
23	chr3:48483400-48486200	Strong transcription	Osteobl	bone
24	chr3:48483400-48486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:48483400-48486400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:48483400-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:48483400-48486400	Strong transcription	Brain Anterior Caudate	brain
28	chr3:48483400-48486400	Strong transcription	Esophagus	oesophagus
29	chr3:48483400-48487200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:48483400-48487200	Weak transcription	Brain Angular Gyrus	brain
31	chr3:48483400-48487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:48483400-48487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:48483600-48484200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:48483600-48484200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:48483600-48484200	Weak transcription	HSMMtube	muscle
36	chr3:48483600-48484400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:48483600-48484400	Genic enhancers	Dnd41	blood
38	chr3:48483600-48484600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:48483600-48484600	Strong transcription	Colonic Mucosa	Colon
40	chr3:48483600-48484600	Genic enhancers	Fetal Intestine Small	intestine
41	chr3:48483600-48484800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:48483600-48485000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:48483600-48485000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:48483600-48485000	Weak transcription	Brain Substantia Nigra	brain
45	chr3:48483600-48485000	Weak transcription	A549	lung
46	chr3:48483600-48485000	Enhancers	HepG2	liver
47	chr3:48483600-48485200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr3:48483600-48485200	Strong transcription	Fetal Lung	lung
49	chr3:48483600-48485200	Strong transcription	Right Ventricle	heart
50	chr3:48483600-48486000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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