Variant report

Variant	rs1459249
Chromosome Location	chr3:48479618-48479619
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	chr3:48479236-48481196	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48477555..48484761-chr3:48484855..48490000,13	MCF-7	breast:
2	chr3:48468825..48473989-chr3:48477233..48479904,8	MCF-7	breast:
3	chr3:48479559..48482051-chr3:48646378..48648594,2	K562	blood:

Variant related genes	Relation type
TMA7	TF binding region
ENSG00000244380	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000164050	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1037773	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10470686	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1109227	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130170	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130171	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712561	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11797	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487542	0.96[EUR][1000 genomes]
rs13069724	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13071337	0.96[EUR][1000 genomes]
rs13072012	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076076	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091785	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13314659	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13324374	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459242	0.91[EUR][1000 genomes]
rs1459250	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563736	0.96[EUR][1000 genomes]
rs1824363	0.97[ASN][1000 genomes]
rs1870444	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975844	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2045554	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242150	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279077	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290822	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2362450	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362452	0.91[EUR][1000 genomes]
rs28824259	0.96[EUR][1000 genomes]
rs2885509	0.91[EUR][1000 genomes]
rs2885510	0.91[EUR][1000 genomes]
rs3214041	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34761139	0.96[EUR][1000 genomes]
rs35215722	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774808	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490383	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858793	0.91[EUR][1000 genomes]
rs4858817	0.91[EUR][1000 genomes]
rs56298324	0.81[EUR][1000 genomes]
rs60512868	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442116	0.90[EUR][1000 genomes]
rs6442117	0.93[EUR][1000 genomes]
rs6442118	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442119	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442120	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442123	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442124	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6764415	0.84[EUR][1000 genomes]
rs6770470	0.96[EUR][1000 genomes]
rs6776700	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779262	0.91[EUR][1000 genomes]
rs6784322	0.94[EUR][1000 genomes]
rs6784541	0.94[EUR][1000 genomes]
rs6794875	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6796491	0.96[EUR][1000 genomes]
rs6800475	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804774	0.96[EUR][1000 genomes]
rs6810060	0.95[EUR][1000 genomes]
rs7126	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725309	0.91[EUR][1000 genomes]
rs725310	0.91[EUR][1000 genomes]
rs73074358	0.96[EUR][1000 genomes]
rs7618883	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630741	0.93[EUR][1000 genomes]
rs7634377	0.94[EUR][1000 genomes]
rs7635522	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7636044	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636782	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7639743	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653691	0.92[EUR][1000 genomes]
rs898225	0.91[EUR][1000 genomes]
rs922075	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311423	0.94[EUR][1000 genomes]
rs9311424	0.94[EUR][1000 genomes]
rs9809843	0.96[EUR][1000 genomes]
rs9812647	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9815103	0.92[EUR][1000 genomes]
rs9817615	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9826195	0.96[EUR][1000 genomes]
rs9826247	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838618	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849509	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9862575	0.96[EUR][1000 genomes]
rs9864371	0.96[EUR][1000 genomes]
rs9864815	0.96[EUR][1000 genomes]
rs9875280	0.96[EUR][1000 genomes]
rs9876781	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876891	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881491	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883759	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883927	0.92[AMR][1000 genomes];0.99[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
rs1459249	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs1459249	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs1459249	TMA7	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48471800-48480800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:48472000-48480600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:48472000-48481000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:48472400-48480200	Weak transcription	Right Atrium	heart
5	chr3:48472400-48480800	Weak transcription	Fetal Brain Male	brain
6	chr3:48474400-48480400	Weak transcription	A549	lung
7	chr3:48475000-48481000	Weak transcription	Brain Angular Gyrus	brain
8	chr3:48475200-48481200	Weak transcription	Left Ventricle	heart
9	chr3:48475400-48480800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:48475400-48481000	Weak transcription	Brain Germinal Matrix	brain
11	chr3:48476000-48480600	Weak transcription	Fetal Lung	lung
12	chr3:48476000-48480800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:48476000-48481000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:48476000-48481000	Weak transcription	NH-A	brain
15	chr3:48476000-48481200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:48476000-48481200	Weak transcription	Aorta	Aorta
17	chr3:48476200-48480000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:48476200-48480400	Weak transcription	Liver	Liver
19	chr3:48476200-48480400	Weak transcription	Fetal Brain Female	brain
20	chr3:48476200-48480800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:48476200-48480800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:48476200-48480800	Weak transcription	Adipose Nuclei	Adipose
23	chr3:48476200-48480800	Weak transcription	Fetal Heart	heart
24	chr3:48476200-48480800	Weak transcription	HSMM	muscle
25	chr3:48476200-48481000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:48476200-48481000	Weak transcription	NHDF-Ad	bronchial
27	chr3:48476200-48481000	Weak transcription	Osteobl	bone
28	chr3:48476400-48480200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:48476400-48480400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:48476400-48480600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:48476400-48480600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:48476400-48480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:48476400-48480800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:48476400-48481000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:48476400-48481000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:48476600-48480200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:48476600-48480200	Weak transcription	Right Ventricle	heart
38	chr3:48476600-48480600	Weak transcription	NHLF	lung
39	chr3:48476600-48481200	Weak transcription	Lung	lung
40	chr3:48476800-48480400	Weak transcription	Primary T cells from cord blood	blood
41	chr3:48476800-48480600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:48476800-48480800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:48477000-48481000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:48477200-48480000	Enhancers	GM12878-XiMat	blood
45	chr3:48477400-48480000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:48477400-48480200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:48477400-48480200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:48477400-48480800	Weak transcription	Fetal Kidney	kidney
49	chr3:48477400-48480800	Weak transcription	HSMMtube	muscle
50	chr3:48477400-48481200	Weak transcription	Esophagus	oesophagus

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