Variant report

Variant	rs7545542
Chromosome Location	chr1:209979635-209979636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:125)
CpG islands
(count:122)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:125 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr1:209978864-209979834	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:209979462-209979855	K562	blood:	n/a	n/a
3	POLR2A	chr1:209979100-209979850	MCF-7	breast:	n/a	n/a
4	HEY1	chr1:209979475-209979878	K562	blood:	n/a	n/a
5	CREB1	chr1:209979282-209979709	ECC-1	luminal epithelium:	n/a	n/a
6	CREB1	chr1:209979230-209979899	K562	blood:	n/a	n/a
7	PAX5	chr1:209979456-209979675	GM12892	blood:	n/a	chr1:209979543-209979562
8	GTF2F1	chr1:209979274-209979820	H1-hESC	embryonic stem cell:	n/a	n/a
9	IRF1	chr1:209979475-209980173	K562	blood:	n/a	chr1:209979523-209979537 chr1:209980083-209980097 chr1:209980081-209980091 chr1:209980081-209980095 chr1:209979542-209979556
10	CREB1	chr1:209979164-209979758	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:209979530-209979833	K562	blood:	n/a	n/a
12	UBTF	chr1:209979425-209980012	K562	blood:	n/a	n/a
13	YY1	chr1:209979427-209979846	K562	blood:	n/a	n/a
14	FOS	chr1:209979365-209979653	MCF10A-Er-Src	breast:	n/a	n/a
15	SP4	chr1:209979169-209979733	H1-hESC	embryonic stem cell:	n/a	chr1:209979542-209979558 chr1:209979544-209979560
16	TAF1	chr1:209979397-209979791	K562	blood:	n/a	n/a
17	FOS	chr1:209979440-209979697	MCF10A-Er-Src	breast:	n/a	n/a
18	YY1	chr1:209979495-209979792	K562	blood:	n/a	n/a
19	MYC	chr1:209979313-209980013	K562	blood:	n/a	n/a
20	POLR2A	chr1:209979087-209980047	PBDE	blood:	n/a	n/a
21	CCNT2	chr1:209979292-209979796	K562	blood:	n/a	n/a
22	MYC	chr1:209979273-209979979	MCF10A-Er-Src	breast:	n/a	n/a
23	MAX	chr1:209979354-209979691	K562	blood:	n/a	n/a
24	MAX	chr1:209979252-209979710	MCF-7	breast:	n/a	n/a
25	STAT3	chr1:209979397-209979780	MCF10A-Er-Src	breast:	n/a	chr1:209979427-209979439
26	TCF12	chr1:209979144-209979991	ECC-1	luminal epithelium:	n/a	chr1:209979536-209979543
27	ZC3H11A	chr1:209979293-209979830	K562	blood:	n/a	n/a
28	ETS1	chr1:209979505-209979772	K562	blood:	n/a	chr1:209979524-209979537 chr1:209979547-209979558
29	POLR2A	chr1:209978698-209980017	H1-hESC	embryonic stem cell:	n/a	n/a
30	TAF7	chr1:209979168-209979887	H1-hESC	embryonic stem cell:	n/a	n/a
31	TBL1XR1	chr1:209979341-209979990	K562	blood:	n/a	n/a
32	FOS	chr1:209979451-209979768	MCF10A-Er-Src	breast:	n/a	n/a
33	EP300	chr1:209979224-209979912	T-47D	breast:	n/a	chr1:209979608-209979624
34	POLR2A	chr1:209979162-209979885	MCF-7	breast:	n/a	n/a
35	POLR2A	chr1:209979372-209979882	HUVEC	blood vessel:	n/a	n/a
36	MAX	chr1:209979190-209979706	H1-hESC	embryonic stem cell:	n/a	n/a
37	STAT3	chr1:209979472-209979767	MCF10A-Er-Src	breast:	n/a	n/a
38	TAF1	chr1:209979109-209979979	ECC-1	luminal epithelium:	n/a	n/a
39	ZEB1	chr1:209979299-209979666	GM12878	blood:	n/a	chr1:209979534-209979545 chr1:209979533-209979545 chr1:209979536-209979545 chr1:209979463-209979472 chr1:209979461-209979472
40	MYC	chr1:209979294-209979787	MCF10A-Er-Src	breast:	n/a	n/a
41	BHLHE40	chr1:209979224-209980048	K562	blood:	n/a	n/a
42	TBP	chr1:209979448-209979964	K562	blood:	n/a	n/a
43	MAX	chr1:209979117-209980080	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr1:209978258-209980648	MCF10A-Er-Src	breast:	n/a	n/a
45	TAF7	chr1:209979239-209979928	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr1:209979170-209979931	HCT-116	colon:	n/a	n/a
47	UBTF	chr1:209979500-209979984	K562	blood:	n/a	n/a
48	ZEB1	chr1:209979164-209979852	GM12878	blood:	n/a	chr1:209979534-209979545 chr1:209979533-209979545 chr1:209979536-209979545 chr1:209979463-209979472 chr1:209979461-209979472
49	IRF1	chr1:209979344-209979960	K562	blood:	n/a	chr1:209979523-209979537 chr1:209979542-209979556
50	FOS	chr1:209979446-209979698	MCF10A-Er-Src	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:209979624-209979674	HCF	heart:	n/a
2	chr1:209979624-209979674	HUVEC	blood vessel:	n/a
3	chr1:209979598-209979648	GM19239	blood:	n/a
4	chr1:209979598-209979648	Hepatocyte	liver:	n/a
5	chr1:209979624-209979674	HCM	heart:	n/a
6	chr1:209979624-209979674	HRE	kidney:	n/a
7	chr1:209979624-209979674	AoSMC	blood vessel:	n/a
8	chr1:209979624-209979674	AG09319	gingival:	n/a
9	chr1:209979598-209979648	PFSK-1	brain:	n/a
10	chr1:209979624-209979674	LNCaP	prostate:	n/a
11	chr1:209979624-209979674	HEK293	kidney:	embryo
12	chr1:209979598-209979648	HIPEpiC	eye:	n/a
13	chr1:209979624-209979674	PrEC	prostate:	n/a
14	chr1:209979624-209979674	PFSK-1	brain:	n/a
15	chr1:209979598-209979648	NHDF-neo	bronchial:	n/a
16	chr1:209979624-209979674	ECC-1	luminal epithelium:	n/a
17	chr1:209979598-209979648	SKMC	muscle:	n/a
18	chr1:209979598-209979648	MCF10A-Er-Src	breast:	n/a
19	chr1:209979624-209979674	HPAEpiC	pulmonary alveolar:	n/a
20	chr1:209979598-209979648	HNPCEpiC	eye:	n/a
21	chr1:209979598-209979648	SAEC	small airway:	n/a
22	chr1:209979624-209979674	SK-N-SH	brain:	n/a
23	chr1:209979624-209979674	NT2-D1	testis:	n/a
24	chr1:209979624-209979674	MCF-7	breast:	n/a
25	chr1:209979598-209979648	HEK293	kidney:	embryo
26	chr1:209979624-209979674	RPTEC	kidney:	n/a
27	chr1:209979598-209979648	GM12891	blood:	n/a
28	chr1:209979624-209979674	Jurkat	blood:	n/a
29	chr1:209979598-209979648	HepG2	liver:	n/a
30	chr1:209979624-209979674	BE2_C	brain:	n/a
31	chr1:209979624-209979674	K562	blood:	n/a
32	chr1:209979624-209979674	HEEpiC	esophagus:	n/a
33	chr1:209979624-209979674	SK-N-MC	brain:	n/a
34	chr1:209979624-209979674	HRPEpiC	eye:	n/a
35	chr1:209979598-209979648	NT2-D1	testis:	n/a
36	chr1:209979624-209979674	HCPEpiC	choroid plexus:	n/a
37	chr1:209979624-209979674	Caco-2	colon:	n/a
38	chr1:209979624-209979674	SKMC	muscle:	n/a
39	chr1:209979598-209979648	HRPEpiC	eye:	n/a
40	chr1:209979598-209979648	MCF-7	breast:	n/a
41	chr1:209979598-209979648	IMR90	lung:	fetal
42	chr1:209979598-209979648	HL-60	blood:	n/a
43	chr1:209979624-209979674	CMK	blood:	n/a
44	chr1:209979624-209979674	Hela-S3	cervix:	n/a
45	chr1:209979598-209979648	NH-A	brain:	n/a
46	chr1:209979598-209979648	RPTEC	kidney:	n/a
47	chr1:209979598-209979648	LNCaP	prostate:	n/a
48	chr1:209979598-209979648	NHBE	bronchial:	n/a
49	chr1:209979624-209979674	IMR90	lung:	fetal
50	chr1:209979624-209979674	HNPCEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr1:209979052..209983681-chr1:210545344..210549112,5	K562	blood:
2	chr1:209977871..209984485-chr1:209998424..210002427,6	K562	blood:
3	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
4	chr1:209956289..209959543-chr1:209978892..209981541,4	K562	blood:
5	chr1:209968649..209970778-chr1:209979506..209982286,2	K562	blood:
6	chr1:209977871..209981214-chr1:209999703..210002866,6	K562	blood:
7	chr1:209974237..209976657-chr1:209978058..209981003,3	K562	blood:

No data

Variant related genes	Relation type
IRF6	TF binding region
IRF6	CpG island
ENSG00000162757	Chromatin interaction
ENSG00000117595	Chromatin interaction
ENSG00000117597	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000232222	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1005287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044516	0.90[LWK][hapmap]
rs1160411	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803382	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs11805830	0.81[AFR][1000 genomes]
rs12403599	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015218	1.00[LWK][hapmap];0.95[YRI][hapmap]
rs17015226	0.96[LWK][hapmap];0.95[YRI][hapmap]
rs17015250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005982	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013162	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073485	0.96[LWK][hapmap];0.95[YRI][hapmap]
rs2073486	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179254	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235372	0.90[LWK][hapmap]
rs2235375	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236907	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294408	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357229	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753518	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs59043219	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6540560	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs6659549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685182	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742215	0.81[LWK][hapmap]
rs7545538	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550857	0.90[LWK][hapmap];0.95[YRI][hapmap]
rs7552506	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs926348	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7545542	IKBKE	cis	parietal	SCAN
rs7545542	SYT14	cis	parietal	SCAN
rs7545542	REN	cis	cerebellum	SCAN
rs7545542	IRF6	cis	Whole Blood	GTEx
rs7545542	IRF6	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209977000-209980000	Active TSS	Esophagus	oesophagus
2	chr1:209977400-209979800	Active TSS	Duodenum Mucosa	Duodenum
3	chr1:209977600-209980200	Flanking Active TSS	HUVEC	blood vessel
4	chr1:209977800-209980000	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:209977800-209980200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:209978000-209980400	Active TSS	Colonic Mucosa	Colon
7	chr1:209978200-209979800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:209978200-209980200	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:209978200-209980400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:209978200-209980400	Active TSS	HMEC	breast
11	chr1:209978400-209979800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:209978400-209979800	Active TSS	Fetal Kidney	kidney
13	chr1:209978400-209980000	Active TSS	H1 Cell Line	embryonic stem cell
14	chr1:209978400-209980000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:209978400-209980000	Flanking Active TSS	Liver	Liver
16	chr1:209978600-209979800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:209978600-209979800	Active TSS	Pancreas	Pancrea
18	chr1:209978600-209979800	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr1:209978600-209980000	Active TSS	Small Intestine	intestine
20	chr1:209978800-209979800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:209978800-209979800	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:209978800-209980000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr1:209978800-209980000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:209978800-209980000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
25	chr1:209979000-209979800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:209979000-209979800	Flanking Active TSS	Placenta	Placenta
27	chr1:209979000-209980000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr1:209979000-209980000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
29	chr1:209979000-209980000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr1:209979000-209980000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:209979000-209980000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:209979000-209980000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:209979000-209980000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr1:209979000-209980400	Active TSS	NHEK	skin
35	chr1:209979200-209979800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:209979200-209979800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:209979200-209979800	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr1:209979200-209979800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:209979200-209979800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
40	chr1:209979200-209979800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
41	chr1:209979200-209979800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
42	chr1:209979200-209979800	Bivalent/Poised TSS	Fetal Brain Female	brain
43	chr1:209979200-209979800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
44	chr1:209979200-209979800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
45	chr1:209979200-209979800	Flanking Active TSS	Lung	lung
46	chr1:209979200-209979800	Flanking Active TSS	Thymus	Thymus
47	chr1:209979200-209979800	ZNF genes & repeats	Spleen	Spleen
48	chr1:209979200-209980000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:209979200-209980000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:209979200-209980000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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