Variant report

Variant	rs10936203
Chromosome Location	chr3:160208092-160208093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:160207812-160208598	A549	lung:	n/a	n/a
2	POLR2A	chr3:160207786-160208214	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:160208002-160208265	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:160208045-160208245	GM12878	blood:	n/a	n/a
5	MAFK	chr3:160208005-160208275	HepG2	liver:	n/a	n/a
6	MAFK	chr3:160207983-160208284	HepG2	liver:	n/a	n/a
7	KAP1	chr3:160208025-160208282	K562	blood:	n/a	n/a
8	FOXA1	chr3:160207925-160208167	T-47D	breast:	n/a	n/a
9	POLR2A	chr3:160207810-160208233	SK-N-MC	brain:	n/a	n/a
10	MAFF	chr3:160207989-160208281	HepG2	liver:	n/a	n/a
11	MAFK	chr3:160208085-160208248	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAFK	chr3:160207961-160208322	IMR90	lung:	n/a	n/a
13	POLR2A	chr3:160207846-160208177	HUVEC	blood vessel:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160204576..160208180-chr3:160214688..160218928,3	MCF-7	breast:
2	chr3:160200027..160203201-chr3:160206463..160209183,3	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM59	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10936201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11708118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11709232	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11711627	0.88[EUR][1000 genomes]
rs11712392	0.83[EUR][1000 genomes]
rs11713230	0.83[EUR][1000 genomes]
rs11716413	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11719750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11720689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11721112	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12152435	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630564	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12630770	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12630956	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12632030	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs12638633	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12639488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13065269	0.83[EUR][1000 genomes]
rs13074231	0.83[EUR][1000 genomes]
rs1369666	0.83[AFR][1000 genomes]
rs16831207	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16831337	0.80[CEU][hapmap]
rs17236494	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17826137	0.83[EUR][1000 genomes]
rs17826173	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17826257	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1873076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1882125	0.90[CHB][hapmap]
rs1920663	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1971128	0.84[AFR][1000 genomes]
rs2095529	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2099496	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2141668	0.84[EUR][1000 genomes]
rs2178451	0.84[EUR][1000 genomes]
rs35008770	0.84[EUR][1000 genomes]
rs35498840	0.90[CHB][hapmap]
rs3732706	0.89[ASW][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs3773369	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3851365	0.81[JPT][hapmap]
rs4133253	0.80[CEU][hapmap]
rs4679886	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4679892	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679903	0.86[EUR][1000 genomes]
rs4679904	0.83[EUR][1000 genomes]
rs4680581	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4680586	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56952700	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60395700	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6441311	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73875254	0.80[AMR][1000 genomes]
rs73875259	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73875285	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875290	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7610939	0.80[CEU][hapmap]
rs7634255	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7644186	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats 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	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10936203	IFT80	cis	parietal	SCAN
rs10936203	IFT80	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160193400-160213000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:160199000-160211600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:160204000-160211200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:160204000-160215800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:160204000-160216000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:160204000-160219000	Weak transcription	Lung	lung
7	chr3:160204000-160219000	Weak transcription	Thymus	Thymus
8	chr3:160204000-160224000	Weak transcription	Gastric	stomach
9	chr3:160204000-160238200	Weak transcription	Small Intestine	intestine
10	chr3:160204200-160209600	Weak transcription	HSMMtube	muscle
11	chr3:160204200-160213200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:160204200-160215600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:160204200-160215800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:160204200-160215800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:160204200-160215800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:160204200-160215800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:160204200-160215800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:160204200-160215800	Weak transcription	Fetal Thymus	thymus
19	chr3:160204200-160215800	Weak transcription	HSMM	muscle
20	chr3:160204200-160215800	Weak transcription	NHDF-Ad	bronchial
21	chr3:160204200-160216000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:160204200-160216000	Weak transcription	Osteobl	bone
23	chr3:160204200-160216200	Weak transcription	Primary T cells from cord blood	blood
24	chr3:160204200-160216200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:160204200-160216200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:160204200-160216200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:160204200-160216200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:160204200-160216200	Weak transcription	Liver	Liver
29	chr3:160204200-160216200	Weak transcription	HMEC	breast
30	chr3:160204200-160216400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:160204200-160216400	Weak transcription	HUVEC	blood vessel
32	chr3:160204200-160216800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:160204200-160217200	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:160204200-160217600	Weak transcription	NH-A	brain
35	chr3:160204200-160218800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:160204200-160218800	Weak transcription	Fetal Intestine Large	intestine
37	chr3:160204200-160219000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:160204200-160219000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:160204200-160219000	Weak transcription	NHEK	skin
40	chr3:160204200-160219200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:160204200-160219200	Weak transcription	Aorta	Aorta
42	chr3:160204200-160219200	Weak transcription	Left Ventricle	heart
43	chr3:160204200-160219400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:160204200-160224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:160204200-160224800	Weak transcription	GM12878-XiMat	blood
46	chr3:160204200-160225400	Weak transcription	Fetal Kidney	kidney
47	chr3:160204400-160215600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:160204400-160215800	Weak transcription	Primary B cells from cord blood	blood
49	chr3:160204400-160216400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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