Variant report

Variant	rs5744545
Chromosome Location	chr5:74808417-74808418
allele	A/G
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	chr5:74806410-74808835	GM18505	blood:	n/a	n/a
2	MAX	chr5:74805816-74808456	NB4	blood:	n/a	n/a
3	CUX1	chr5:74807648-74808553	K562	blood:	n/a	n/a
4	POLR2A	chr5:74806479-74808595	PBDE	blood:	n/a	n/a
5	CEBPB	chr5:74808219-74808557	A549	lung:	n/a	chr5:74808391-74808404 chr5:74808392-74808403 chr5:74808391-74808402 chr5:74808391-74808402
6	TBL1XR1	chr5:74807269-74808517	K562	blood:	n/a	n/a
7	POLR2A	chr5:74806345-74808532	GM18951	blood:	n/a	n/a
8	FOS	chr5:74808235-74808526	MCF10A-Er-Src	breast:	n/a	n/a
9	RUNX3	chr5:74807210-74808465	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:74806603-74808536	GM12878	blood:	n/a	n/a
11	ZNF143	chr5:74807264-74808429	K562	blood:	n/a	chr5:74807697-74807716 chr5:74807702-74807720 chr5:74807711-74807720 chr5:74807709-74807718
12	CHD1	chr5:74805200-74808587	GM12878	blood:	n/a	chr5:74806845-74806855
13	TBP	chr5:74807237-74808529	GM12878	blood:	n/a	n/a
14	SIN3A	chr5:74807095-74808436	GM12878	blood:	n/a	n/a
15	CEBPB	chr5:74808218-74808567	IMR90	lung:	n/a	chr5:74808391-74808404 chr5:74808392-74808403 chr5:74808391-74808402 chr5:74808391-74808402
16	TBL1XR1	chr5:74807090-74808522	GM12878	blood:	n/a	n/a
17	MXI1	chr5:74805703-74808471	GM12878	blood:	n/a	n/a
18	IRF1	chr5:74807266-74808454	K562	blood:	n/a	chr5:74807372-74807381 chr5:74807350-74807370
19	CEBPB	chr5:74808324-74808484	HepG2	liver:	n/a	chr5:74808391-74808404 chr5:74808392-74808403 chr5:74808391-74808402 chr5:74808391-74808402
20	RUNX3	chr5:74807187-74808520	GM12878	blood:	n/a	n/a
21	RCOR1	chr5:74807275-74808845	K562	blood:	n/a	n/a
22	POLR2A	chr5:74806398-74808422	GM19099	blood:	n/a	n/a
23	CEBPB	chr5:74808231-74808522	K562	blood:	n/a	chr5:74808391-74808404 chr5:74808392-74808403 chr5:74808391-74808402 chr5:74808391-74808402
24	POLR2A	chr5:74806472-74808593	GM18526	blood:	n/a	n/a
25	CEBPB	chr5:74808162-74808597	K562	blood:	n/a	chr5:74808391-74808404 chr5:74808392-74808403 chr5:74808391-74808402 chr5:74808391-74808402
26	POLR2A	chr5:74807206-74808916	GM12891	blood:	n/a	n/a
27	STAT3	chr5:74808305-74808525	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr5:74806448-74808483	IMR90	lung:	n/a	n/a
29	MTA3	chr5:74806454-74808806	GM12878	blood:	n/a	n/a
30	STAT3	chr5:74808199-74808536	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr5:74807198-74808455	MCF10A-Er-Src	breast:	n/a	n/a
32	TBP	chr5:74807165-74808493	K562	blood:	n/a	n/a
33	MYC	chr5:74807238-74808457	NB4	blood:	n/a	n/a
34	FOXA1	chr5:74808230-74808591	HepG2	liver:	n/a	n/a
35	POLR2A	chr5:74806443-74808463	GM12892	blood:	n/a	n/a
36	SREBP1	chr5:74807187-74809330	GM12878	blood:	n/a	n/a
37	FOXA2	chr5:74808283-74808499	HepG2	liver:	n/a	n/a
38	POLR2A	chr5:74807250-74808521	K562	blood:	n/a	n/a
39	POLR2A	chr5:74806449-74808485	GM12878	blood:	n/a	n/a
40	CEBPB	chr5:74807767-74808590	K562	blood:	n/a	chr5:74808391-74808404 chr5:74808392-74808403 chr5:74808391-74808402 chr5:74808391-74808402
41	HCFC1	chr5:74805817-74808663	Hela-S3	cervix:	n/a	n/a
42	ATF2	chr5:74807091-74808445	GM12878	blood:	n/a	n/a
43	POLR2A	chr5:74806447-74808472	GM19193	blood:	n/a	n/a
44	CEBPB	chr5:74807369-74808581	Hela-S3	cervix:	n/a	chr5:74808391-74808404 chr5:74808392-74808403 chr5:74808391-74808402 chr5:74808391-74808402
45	CEBPB	chr5:74808212-74808574	HepG2	liver:	n/a	chr5:74808391-74808404 chr5:74808392-74808403 chr5:74808391-74808402 chr5:74808391-74808402

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74806025..74808781-chr5:74906137..74908952,2	MCF-7	breast:
2	chr5:74808217..74810593-chr5:74816041..74817596,2	K562	blood:

Variant related genes	Relation type
COL4A3BP	TF binding region
ENSG00000189045	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10036682	0.89[EUR][1000 genomes]
rs10038945	0.89[EUR][1000 genomes]
rs10041470	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10055011	0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10059022	0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10061689	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10067900	0.86[EUR][1000 genomes]
rs10074747	0.85[EUR][1000 genomes]
rs10076819	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10077427	0.89[EUR][1000 genomes]
rs10078671	0.89[EUR][1000 genomes]
rs10474437	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12173076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13360099	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13361353	0.89[EUR][1000 genomes]
rs1469051	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1553234	0.89[EUR][1000 genomes]
rs1820049	0.88[EUR][1000 genomes]
rs1909719	0.89[EUR][1000 genomes]
rs2287710	0.88[EUR][1000 genomes]
rs253387	0.86[JPT][hapmap]
rs253410	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs28408106	0.86[EUR][1000 genomes]
rs28612248	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28668361	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28874007	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34355	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs34356	0.85[JPT][hapmap]
rs34357	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs3804231	0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs4703671	0.84[EUR][1000 genomes]
rs4703675	0.89[EUR][1000 genomes]
rs4704213	0.86[EUR][1000 genomes]
rs4704229	0.92[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs56859362	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744544	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5744636	0.89[EUR][1000 genomes]
rs5744667	0.86[EUR][1000 genomes]
rs5744704	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5744709	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5744712	0.85[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs57907925	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58519566	0.86[EUR][1000 genomes]
rs58841453	0.89[EUR][1000 genomes]
rs61303403	0.82[EUR][1000 genomes]
rs6891560	0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72633964	0.86[EUR][1000 genomes]
rs72633965	0.86[EUR][1000 genomes]
rs72633967	0.84[EUR][1000 genomes]
rs72633968	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72633969	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72633970	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72633971	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72633972	0.87[EUR][1000 genomes]
rs72633973	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72633974	0.89[EUR][1000 genomes]
rs72633975	0.89[EUR][1000 genomes]
rs72633976	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72633977	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7356633	0.86[EUR][1000 genomes]
rs7726478	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs904743	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9293652	0.86[EUR][1000 genomes]
rs9293654	0.83[EUR][1000 genomes]
rs9293655	0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs979182	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv882200	chr5:74781439-74830808	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv882201	chr5:74787310-74890618	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5744545	ARSB	cis	parietal	SCAN
rs5744545	TNPO1	cis	cerebellum	SCAN
rs5744545	GCNT4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74804000-74809000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:74804600-74808600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:74804600-74809800	Active TSS	NHLF	lung
4	chr5:74804800-74809600	Active TSS	K562	blood
5	chr5:74805000-74808600	Active TSS	Fetal Stomach	stomach
6	chr5:74805000-74810200	Active TSS	GM12878-XiMat	blood
7	chr5:74805200-74808600	Active TSS	HSMMtube	muscle
8	chr5:74805200-74809000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:74805200-74809000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:74805200-74809000	Active TSS	NHDF-Ad	bronchial
11	chr5:74805200-74809400	Active TSS	Right Atrium	heart
12	chr5:74805400-74808600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:74805400-74808600	Active TSS	Fetal Intestine Large	intestine
14	chr5:74805400-74808600	Active TSS	Right Ventricle	heart
15	chr5:74805400-74808600	Active TSS	HMEC	breast
16	chr5:74805400-74809000	Active TSS	Ovary	ovary
17	chr5:74805400-74809200	Active TSS	HSMM	muscle
18	chr5:74805400-74809400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:74805600-74808600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr5:74805600-74808600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:74805600-74808600	Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr5:74805600-74808600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr5:74805600-74808600	Active TSS	Psoas Muscle	Psoas
24	chr5:74805600-74808800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:74805600-74808800	Active TSS	Aorta	Aorta
26	chr5:74805800-74808600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:74805800-74808600	Active TSS	Colonic Mucosa	Colon
28	chr5:74805800-74808600	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr5:74805800-74808600	Active TSS	Fetal Muscle Trunk	muscle
30	chr5:74805800-74808800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:74805800-74808800	Active TSS	Stomach Smooth Muscle	stomach
32	chr5:74805800-74809000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr5:74806000-74808600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr5:74806000-74808600	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr5:74806000-74808600	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr5:74806000-74808600	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr5:74806000-74808600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:74806000-74808600	Active TSS	Colon Smooth Muscle	Colon
39	chr5:74806000-74808600	Active TSS	Placenta	Placenta
40	chr5:74806000-74808600	Active TSS	Fetal Thymus	thymus
41	chr5:74806000-74808600	Active TSS	A549	lung
42	chr5:74806000-74808800	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr5:74806000-74809000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:74806200-74808600	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr5:74806200-74808600	Active TSS	Fetal Muscle Leg	muscle
46	chr5:74806200-74808600	Active TSS	Thymus	Thymus
47	chr5:74807000-74808600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:74807200-74809600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:74807400-74808600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:74807400-74808800	Active TSS	Brain Germinal Matrix	brain

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