Variant report

Variant	rs7639743
Chromosome Location	chr3:48482506-48482507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:48480749-48482635	SK-N-SH	brain:	n/a	n/a
2	PAX5	chr3:48482410-48482629	GM12878	blood:	n/a	n/a
3	HCFC1	chr3:48480876-48482618	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:48480984-48482518	Hela-S3	cervix:	n/a	n/a
5	PML	chr3:48480965-48482528	GM12878	blood:	n/a	n/a
6	MXI1	chr3:48481000-48482513	IMR90	lung:	n/a	n/a
7	POLR2A	chr3:48482001-48483032	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

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	chr3:48228981..48231650-chr3:48479872..48482975,4	K562	blood:
4	chr3:48481215..48483251-chr3:48514789..48517662,2	K562	blood:
5	chr3:48468569..48471339-chr3:48481498..48483135,2	MCF-7	breast:
6	chr3:48481270..48483185-chr3:48591513..48595174,3	MCF-7	breast:
7	chr3:48228981..48231519-chr3:48480145..48483056,4	K562	blood:

No data

Variant related genes	Relation type
CCDC51	TF binding region
ENSG00000164050	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000164045	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];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10470686	0.91[EUR][1000 genomes]
rs1109227	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130170	0.91[EUR][1000 genomes]
rs11130171	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712561	0.89[EUR][1000 genomes]
rs11797	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12487542	0.89[EUR][1000 genomes]
rs13069724	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13071337	0.90[EUR][1000 genomes]
rs13072012	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13076076	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13091785	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13314659	0.91[EUR][1000 genomes]
rs13324374	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1459242	0.84[EUR][1000 genomes]
rs1459249	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1459250	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563736	0.90[EUR][1000 genomes]
rs1824363	0.87[ASN][1000 genomes]
rs1870444	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1975844	0.90[EUR][1000 genomes]
rs2045554	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2242150	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279077	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2290822	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2362450	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2362452	0.84[EUR][1000 genomes]
rs28824259	0.90[EUR][1000 genomes]
rs2885509	0.85[EUR][1000 genomes]
rs2885510	0.85[EUR][1000 genomes]
rs3214041	0.91[EUR][1000 genomes]
rs34761139	0.90[EUR][1000 genomes]
rs35215722	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3774808	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4490383	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858793	0.85[EUR][1000 genomes]
rs4858817	0.85[EUR][1000 genomes]
rs60512868	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442116	0.84[EUR][1000 genomes]
rs6442117	0.87[EUR][1000 genomes]
rs6442118	0.91[EUR][1000 genomes]
rs6442119	0.91[EUR][1000 genomes]
rs6442120	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442123	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442124	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6764415	0.83[AMR][1000 genomes]
rs6770470	0.89[EUR][1000 genomes]
rs6776700	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6779262	0.85[EUR][1000 genomes]
rs6784322	0.88[EUR][1000 genomes]
rs6784541	0.88[EUR][1000 genomes]
rs6794875	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6796491	0.90[EUR][1000 genomes]
rs6800475	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804774	0.90[EUR][1000 genomes]
rs6810060	0.89[EUR][1000 genomes]
rs7126	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs725309	0.85[EUR][1000 genomes]
rs725310	0.85[EUR][1000 genomes]
rs73074358	0.89[EUR][1000 genomes]
rs7618883	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7630741	0.86[EUR][1000 genomes]
rs7634377	0.88[EUR][1000 genomes]
rs7635522	0.89[EUR][1000 genomes]
rs7636044	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7636782	0.87[EUR][1000 genomes]
rs7653691	0.86[EUR][1000 genomes]
rs898225	0.84[EUR][1000 genomes]
rs922075	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311423	0.88[EUR][1000 genomes]
rs9311424	0.88[EUR][1000 genomes]
rs9809843	0.90[EUR][1000 genomes]
rs9812647	0.91[EUR][1000 genomes]
rs9815103	0.86[EUR][1000 genomes]
rs9817615	0.86[ASN][1000 genomes]
rs9826195	0.90[EUR][1000 genomes]
rs9826247	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9838618	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849509	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9862575	0.90[EUR][1000 genomes]
rs9864371	0.90[EUR][1000 genomes]
rs9864815	0.90[EUR][1000 genomes]
rs9875280	0.90[EUR][1000 genomes]
rs9876781	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9876891	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9881491	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9883759	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9883927	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[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
rs7639743	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs7639743	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs7639743	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	chr3:48480200-48482600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr3:48480200-48482800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:48480200-48483400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:48480400-48482800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:48480400-48483000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:48480600-48482800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:48480600-48482800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:48480600-48482800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:48480600-48482800	Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr3:48480600-48482800	Active TSS	NHLF	lung
11	chr3:48480600-48483000	Active TSS	HMEC	breast
12	chr3:48480800-48482600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:48480800-48482600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:48480800-48482600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:48480800-48482800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:48480800-48482800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:48480800-48482800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:48480800-48482800	Active TSS	Fetal Intestine Large	intestine
19	chr3:48480800-48482800	Active TSS	Fetal Kidney	kidney
20	chr3:48480800-48482800	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:48480800-48482800	Active TSS	GM12878-XiMat	blood
22	chr3:48480800-48482800	Active TSS	Hela-S3	cervix
23	chr3:48480800-48483000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:48480800-48483000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr3:48480800-48483000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:48480800-48483000	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr3:48480800-48483000	Active TSS	A549	lung
28	chr3:48480800-48483000	Active TSS	HSMM	muscle
29	chr3:48480800-48483000	Active TSS	HSMMtube	muscle
30	chr3:48480800-48483000	Active TSS	K562	blood
31	chr3:48481000-48482600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:48481000-48482600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:48481000-48482600	Active TSS	Brain Angular Gyrus	brain
34	chr3:48481000-48482600	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr3:48481000-48482800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:48481000-48482800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:48481000-48482800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:48481000-48482800	Active TSS	Muscle Satellite Cultured Cells	--
39	chr3:48481000-48482800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:48481000-48482800	Active TSS	Brain Hippocampus Middle	brain
41	chr3:48481000-48482800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:48481000-48482800	Active TSS	Fetal Intestine Small	intestine
43	chr3:48481000-48482800	Active TSS	Psoas Muscle	Psoas
44	chr3:48481000-48482800	Active TSS	NHEK	skin
45	chr3:48481000-48483000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr3:48481000-48483000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:48481000-48483000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:48481000-48483000	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr3:48481000-48483000	Active TSS	Right Ventricle	heart
50	chr3:48481000-48483000	Active TSS	NHDF-Ad	bronchial

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