Variant report

Variant	rs1037773
Chromosome Location	chr3:48467902-48467903
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:4)
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	HEY1	chr3:48467668-48467989	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:48466790-48473062	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48466636-48473218	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:48461949-48470573	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:48467687-48468079	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:48467378-48467971	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr3:48467840-48467990	GM12873	blood:	n/a	n/a
8	POLR2A	chr3:48467852-48468104	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:48467142-48468379	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:48466832-48470960	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48449710..48451391-chr3:48467472..48469185,2	MCF-7	breast:
2	chr3:48342140..48344321-chr3:48467110..48469904,2	K562	blood:
3	chr3:48445903..48449635-chr3:48463351..48467956,4	MCF-7	breast:
4	chr3:48411970..48413928-chr3:48466299..48468929,2	MCF-7	breast:

No data

Variant related genes	Relation type
PLXNB1	TF binding region
ENSG00000164050	Chromatin interaction
ENSG00000172113	Chromatin interaction
ENSG00000164049	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10470686	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1109227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130170	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712561	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11797	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12487542	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13069724	1.00[CEU][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13071337	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13072012	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13076076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13091785	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13314659	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13324374	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1459242	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs1459249	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1459250	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1563736	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1824363	0.94[ASN][1000 genomes]
rs1870444	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1975844	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2045554	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2362450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362452	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs28824259	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2885509	0.92[EUR][1000 genomes]
rs2885510	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs3214041	1.00[CEU][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34761139	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35215722	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3774808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4490383	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858793	0.92[EUR][1000 genomes]
rs4858795	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs4858817	0.92[EUR][1000 genomes]
rs4858819	0.90[JPT][hapmap]
rs56298324	0.82[EUR][1000 genomes]
rs60512868	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442116	0.91[EUR][1000 genomes]
rs6442117	0.89[CEU][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442118	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442119	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442123	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442124	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6764415	0.84[EUR][1000 genomes]
rs6770470	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6776700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6779262	0.92[EUR][1000 genomes]
rs6784322	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6784541	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6796491	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6800475	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6804774	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6810060	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7126	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725309	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs725310	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs730566	0.90[JPT][hapmap]
rs73074358	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs734071	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7618883	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7630741	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7634377	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7635522	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636044	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636782	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7639743	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651407	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7653691	0.93[EUR][1000 genomes]
rs898225	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs922075	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311423	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9311424	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9311428	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs9809843	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9812647	1.00[CEU][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9815103	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9817615	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826195	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9826247	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9838618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9862575	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9864371	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9864815	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9875280	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9876781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876891	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881491	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9883759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1037773	TMA7	cis	Muscle Skeletal	GTEx
rs1037773	PLXNB1	cis	multi-tissue	Pritchard
rs1037773	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs1037773	RP11-24C3.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48444400-48468600	Weak transcription	HUVEC	blood vessel
2	chr3:48454200-48469000	Weak transcription	Hela-S3	cervix
3	chr3:48457400-48468800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:48459800-48468800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:48462600-48469600	Enhancers	Left Ventricle	heart
6	chr3:48463800-48469200	Enhancers	Stomach Mucosa	stomach
7	chr3:48464800-48468400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:48465000-48468200	Enhancers	Fetal Brain Male	brain
9	chr3:48465000-48469000	Enhancers	Right Ventricle	heart
10	chr3:48465200-48468000	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr3:48465400-48468800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:48465400-48469000	Weak transcription	Thymus	Thymus
13	chr3:48465400-48469200	Enhancers	Fetal Muscle Trunk	muscle
14	chr3:48465800-48468000	Enhancers	Ovary	ovary
15	chr3:48465800-48468800	Genic enhancers	Fetal Stomach	stomach
16	chr3:48466000-48468000	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr3:48466000-48468400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:48466000-48468400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:48466000-48468600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:48466000-48468600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:48466000-48469000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:48466000-48469000	Enhancers	Fetal Lung	lung
23	chr3:48466000-48469400	Enhancers	Fetal Muscle Leg	muscle
24	chr3:48466000-48469400	Enhancers	Lung	lung
25	chr3:48466200-48468200	Enhancers	Liver	Liver
26	chr3:48466200-48468400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:48466200-48468400	Enhancers	Right Atrium	heart
28	chr3:48466200-48470000	Enhancers	Spleen	Spleen
29	chr3:48466400-48469200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:48466400-48469600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:48466400-48470000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:48466400-48470000	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr3:48466600-48468000	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr3:48466600-48468400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr3:48466600-48468400	Enhancers	NHLF	lung
36	chr3:48466600-48468600	Enhancers	Fetal Intestine Large	intestine
37	chr3:48466600-48469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:48466600-48469200	Enhancers	NH-A	brain
39	chr3:48466600-48469600	Enhancers	Gastric	stomach
40	chr3:48466600-48469800	Enhancers	Placenta Amnion	Placenta Amnion
41	chr3:48466600-48470000	Enhancers	Placenta	Placenta
42	chr3:48466800-48468000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:48466800-48468200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr3:48466800-48468400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:48466800-48468800	Enhancers	Pancreas	Pancrea
46	chr3:48466800-48469000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:48466800-48469200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr3:48466800-48469200	Enhancers	A549	lung
49	chr3:48466800-48469400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:48466800-48469800	Flanking Active TSS	Fetal Brain Female	brain

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