Variant report

Variant	rs9883759
Chromosome Location	chr3:48463618-48463619
allele	A/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	chr3:48463421-48463986	HepG2	liver:	n/a	n/a
2	CTCF	chr3:48463565-48463985	HepG2	liver:	n/a	chr3:48463697-48463710
3	POLR2A	chr3:48461949-48470573	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:48463519-48464233	HepG2	liver:	n/a	n/a
5	CTCF	chr3:48463600-48463750	HRE	kidney:	n/a	chr3:48463697-48463710
6	CTCF	chr3:48463560-48463710	HFF-Myc	foreskin:	n/a	chr3:48463697-48463710
7	POLR2A	chr3:48463458-48463892	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:48463425-48465467	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:48462368-48463836	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:48463571-48463917	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48457719..48460304-chr3:48461947..48464533,2	MCF-7	breast:
2	chr3:48445903..48449635-chr3:48463351..48467956,4	MCF-7	breast:
3	chr3:48458996..48461252-chr3:48463522..48466365,3	K562	blood:
4	chr3:48452569..48455000-chr3:48461462..48463973,2	MCF-7	breast:

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

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1037773	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]
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[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130170	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712561	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11797	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12487542	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13069724	1.00[CEU][hapmap];0.96[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];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13091785	0.93[AFR][1000 genomes];0.95[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	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1459242	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs1459249	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1459250	0.94[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	0.80[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];0.83[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[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2362450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362452	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs28824259	0.81[AFR][1000 genomes];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];0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34761139	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35215722	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3774808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4490383	0.87[AMR][1000 genomes];0.94[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	0.88[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442123	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442124	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6764415	0.85[EUR][1000 genomes]
rs6770470	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6776700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[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];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6796491	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6800475	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6804774	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6810060	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7126	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs734071	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7618883	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7630741	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7634377	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7635522	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636044	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636782	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7639743	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651407	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs7653691	0.93[EUR][1000 genomes]
rs898225	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[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	0.81[AFR][1000 genomes];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];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9817615	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826195	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9826247	0.93[AFR][1000 genomes];0.92[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];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9864815	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9875280	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9876781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876891	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881491	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9883927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9883759	PLXNB1	cis	multi-tissue	Pritchard
rs9883759	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs9883759	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs9883759	TMA7	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48442000-48466200	Strong transcription	Fetal Intestine Small	intestine
2	chr3:48442000-48467400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:48442200-48464600	Strong transcription	Brain Germinal Matrix	brain
4	chr3:48442200-48466800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:48442600-48466600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:48443000-48464800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:48443000-48467000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:48443200-48466400	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr3:48443600-48463800	Strong transcription	HepG2	liver
10	chr3:48443800-48465800	Strong transcription	Fetal Intestine Large	intestine
11	chr3:48443800-48466000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:48443800-48466000	Strong transcription	Fetal Brain Female	brain
13	chr3:48443800-48466400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:48443800-48466400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:48443800-48466600	Weak transcription	NH-A	brain
16	chr3:48444000-48464200	Strong transcription	Lung	lung
17	chr3:48444000-48464400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:48444000-48465800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr3:48444000-48466000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:48444000-48466000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:48444400-48465000	Weak transcription	Fetal Brain Male	brain
22	chr3:48444400-48466000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:48444400-48466200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:48444400-48466200	Weak transcription	Right Atrium	heart
25	chr3:48444400-48467200	Weak transcription	NHDF-Ad	bronchial
26	chr3:48444400-48468600	Weak transcription	HUVEC	blood vessel
27	chr3:48444600-48465400	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr3:48444600-48465800	Strong transcription	Fetal Stomach	stomach
29	chr3:48444600-48466200	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr3:48444800-48463800	Strong transcription	Gastric	stomach
31	chr3:48445000-48464600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:48445200-48464000	Strong transcription	Pancreas	Pancrea
33	chr3:48447400-48465200	Weak transcription	Fetal Heart	heart
34	chr3:48449800-48466400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:48451000-48467000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:48451400-48466800	Weak transcription	A549	lung
37	chr3:48454200-48469000	Weak transcription	Hela-S3	cervix
38	chr3:48454400-48464200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:48454600-48463800	Weak transcription	Stomach Mucosa	stomach
40	chr3:48455400-48464000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:48456600-48463800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:48456600-48467600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:48456800-48467200	Weak transcription	Small Intestine	intestine
44	chr3:48457000-48463800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:48457400-48468800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:48458800-48463800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:48458800-48467400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:48459600-48464400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:48459800-48468800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:48460200-48466400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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