Variant report

Variant	rs12403006
Chromosome Location	chr1:209979518-209979519
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:124)
CpG islands
(count:122)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:124 , 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	UBTF	chr1:209979425-209980012	K562	blood:	n/a	n/a
12	YY1	chr1:209979427-209979846	K562	blood:	n/a	n/a
13	FOS	chr1:209979365-209979653	MCF10A-Er-Src	breast:	n/a	n/a
14	SP4	chr1:209979169-209979733	H1-hESC	embryonic stem cell:	n/a	chr1:209979542-209979558 chr1:209979544-209979560
15	TAF1	chr1:209979397-209979791	K562	blood:	n/a	n/a
16	FOS	chr1:209979440-209979697	MCF10A-Er-Src	breast:	n/a	n/a
17	YY1	chr1:209979495-209979792	K562	blood:	n/a	n/a
18	MYC	chr1:209979313-209980013	K562	blood:	n/a	n/a
19	ATF2	chr1:209979190-209979565	H1-hESC	embryonic stem cell:	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	MYC	chr1:209979243-209979587	MCF-7	breast:	n/a	n/a
24	MAX	chr1:209979354-209979691	K562	blood:	n/a	n/a
25	MAX	chr1:209979252-209979710	MCF-7	breast:	n/a	n/a
26	STAT3	chr1:209979397-209979780	MCF10A-Er-Src	breast:	n/a	chr1:209979427-209979439
27	TCF12	chr1:209979144-209979991	ECC-1	luminal epithelium:	n/a	chr1:209979536-209979543
28	ZC3H11A	chr1:209979293-209979830	K562	blood:	n/a	n/a
29	ETS1	chr1:209979505-209979772	K562	blood:	n/a	chr1:209979524-209979537 chr1:209979547-209979558
30	POLR2A	chr1:209978698-209980017	H1-hESC	embryonic stem cell:	n/a	n/a
31	TAF7	chr1:209979168-209979887	H1-hESC	embryonic stem cell:	n/a	n/a
32	TBL1XR1	chr1:209979341-209979990	K562	blood:	n/a	n/a
33	FOS	chr1:209979451-209979768	MCF10A-Er-Src	breast:	n/a	n/a
34	EP300	chr1:209979224-209979912	T-47D	breast:	n/a	chr1:209979608-209979624
35	POLR2A	chr1:209979162-209979885	MCF-7	breast:	n/a	n/a
36	POLR2A	chr1:209979372-209979882	HUVEC	blood vessel:	n/a	n/a
37	MAX	chr1:209979190-209979706	H1-hESC	embryonic stem cell:	n/a	n/a
38	STAT3	chr1:209979472-209979767	MCF10A-Er-Src	breast:	n/a	n/a
39	JUND	chr1:209979342-209979544	H1-hESC	embryonic stem cell:	n/a	n/a
40	TAF1	chr1:209979109-209979979	ECC-1	luminal epithelium:	n/a	n/a
41	ZEB1	chr1:209979299-209979666	GM12878	blood:	n/a	chr1:209979534-209979545 chr1:209979533-209979545 chr1:209979536-209979545 chr1:209979463-209979472 chr1:209979461-209979472
42	MYC	chr1:209979294-209979787	MCF10A-Er-Src	breast:	n/a	n/a
43	BHLHE40	chr1:209979224-209980048	K562	blood:	n/a	n/a
44	TBP	chr1:209979448-209979964	K562	blood:	n/a	n/a
45	MAX	chr1:209979117-209980080	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr1:209978258-209980648	MCF10A-Er-Src	breast:	n/a	n/a
47	TAF7	chr1:209979239-209979928	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr1:209979170-209979931	HCT-116	colon:	n/a	n/a
49	UBTF	chr1:209979500-209979984	K562	blood:	n/a	n/a
50	ZEB1	chr1:209979164-209979852	GM12878	blood:	n/a	chr1:209979534-209979545 chr1:209979533-209979545 chr1:209979536-209979545 chr1:209979463-209979472 chr1:209979461-209979472

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:209979470-209979520	SK-N-SH_RA	brain:	n/a
2	chr1:209979470-209979520	HRPEpiC	eye:	n/a
3	chr1:209979487-209979537	BE2_C	brain:	n/a
4	chr1:209979487-209979537	SKMC	muscle:	n/a
5	chr1:209979487-209979537	NB4	blood:	n/a
6	chr1:209979487-209979537	BJ	skin:	n/a
7	chr1:209979470-209979520	ECC-1	luminal epithelium:	n/a
8	chr1:209979487-209979537	HRE	kidney:	n/a
9	chr1:209979470-209979520	BJ	skin:	n/a
10	chr1:209979470-209979520	HCPEpiC	choroid plexus:	n/a
11	chr1:209979470-209979520	NT2-D1	testis:	n/a
12	chr1:209979487-209979537	GM12878	blood:	n/a
13	chr1:209979487-209979537	SK-N-MC	brain:	n/a
14	chr1:209979470-209979520	GM12891	blood:	n/a
15	chr1:209979487-209979537	HL-60	blood:	n/a
16	chr1:209979470-209979520	HCT-116	colon:	n/a
17	chr1:209979470-209979520	HMEC	breast:	n/a
18	chr1:209979470-209979520	LNCaP	prostate:	n/a
19	chr1:209979470-209979520	NH-A	brain:	n/a
20	chr1:209979487-209979537	AG09319	gingival:	n/a
21	chr1:209979487-209979537	SK-N-SH_RA	brain:	n/a
22	chr1:209979470-209979520	RPTEC	kidney:	n/a
23	chr1:209979470-209979520	HPAEpiC	pulmonary alveolar:	n/a
24	chr1:209979470-209979520	NHBE	bronchial:	n/a
25	chr1:209979487-209979537	AG10803	skin:	n/a
26	chr1:209979470-209979520	SAEC	small airway:	n/a
27	chr1:209979487-209979537	NHBE	bronchial:	n/a
28	chr1:209979487-209979537	MCF-7	breast:	n/a
29	chr1:209979487-209979537	GM12892	blood:	n/a
30	chr1:209979470-209979520	HEK293	kidney:	embryo
31	chr1:209979470-209979520	HCM	heart:	n/a
32	chr1:209979487-209979537	SK-N-SH	brain:	n/a
33	chr1:209979470-209979520	AoSMC	blood vessel:	n/a
34	chr1:209979470-209979520	PANC-1	pancreas:	n/a
35	chr1:209979487-209979537	HIPEpiC	eye:	n/a
36	chr1:209979470-209979520	NB4	blood:	n/a
37	chr1:209979470-209979520	Hepatocyte	liver:	n/a
38	chr1:209979487-209979537	GM06990	blood:	n/a
39	chr1:209979487-209979537	HCPEpiC	choroid plexus:	n/a
40	chr1:209979487-209979537	RPTEC	kidney:	n/a
41	chr1:209979470-209979520	T-47D	breast:	n/a
42	chr1:209979487-209979537	ECC-1	luminal epithelium:	n/a
43	chr1:209979470-209979520	SK-N-SH	brain:	n/a
44	chr1:209979470-209979520	H1-hESC	embryonic stem cell:	embryo
45	chr1:209979487-209979537	HPAEpiC	pulmonary alveolar:	n/a
46	chr1:209979470-209979520	BE2_C	brain:	n/a
47	chr1:209979470-209979520	HIPEpiC	eye:	n/a
48	chr1:209979470-209979520	ProgFib	skin:	n/a
49	chr1:209979487-209979537	Hepatocyte	liver:	n/a
50	chr1:209979487-209979537	ovcar-3	ovarian:	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
ENSG00000117597	Chromatin interaction
ENSG00000162757	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000232222	Chromatin interaction
ENSG00000117595	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10127937	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10218448	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10489344	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11119354	0.84[ASN][1000 genomes]
rs11582607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584081	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11590807	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11810091	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12404886	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17317580	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17389541	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013196	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601717	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34743335	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753510	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753513	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766615	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41274838	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240837	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56071308	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56268268	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61820635	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6699507	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72741048	0.89[EUR][1000 genomes]
rs7526313	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544804	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546104	0.84[ASN][1000 genomes]
rs932334	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12403006	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:120 , 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	chr1:209977800-209979600	Active TSS	Fetal Intestine Large	intestine
5	chr1:209977800-209979600	Active TSS	Gastric	stomach
6	chr1:209977800-209980000	Active TSS	Rectal Smooth Muscle	rectum
7	chr1:209977800-209980200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:209978000-209979600	Active TSS	Fetal Intestine Small	intestine
9	chr1:209978000-209980400	Active TSS	Colonic Mucosa	Colon
10	chr1:209978200-209979800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr1:209978200-209980200	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr1:209978200-209980400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:209978200-209980400	Active TSS	HMEC	breast
14	chr1:209978400-209979600	Active TSS	Stomach Mucosa	stomach
15	chr1:209978400-209979800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr1:209978400-209979800	Active TSS	Fetal Kidney	kidney
17	chr1:209978400-209980000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr1:209978400-209980000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:209978400-209980000	Flanking Active TSS	Liver	Liver
20	chr1:209978600-209979600	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr1:209978600-209979600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:209978600-209979600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
23	chr1:209978600-209979800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:209978600-209979800	Active TSS	Pancreas	Pancrea
25	chr1:209978600-209979800	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr1:209978600-209980000	Active TSS	Small Intestine	intestine
27	chr1:209978800-209979600	Active TSS	Osteobl	bone
28	chr1:209978800-209979800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:209978800-209979800	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr1:209978800-209980000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr1:209978800-209980000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:209978800-209980000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
33	chr1:209979000-209979600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:209979000-209979600	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr1:209979000-209979600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
36	chr1:209979000-209979600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:209979000-209979800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:209979000-209979800	Flanking Active TSS	Placenta	Placenta
39	chr1:209979000-209980000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr1:209979000-209980000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
41	chr1:209979000-209980000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr1:209979000-209980000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:209979000-209980000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:209979000-209980000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:209979000-209980000	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr1:209979000-209980400	Active TSS	NHEK	skin
47	chr1:209979200-209979600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:209979200-209979600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:209979200-209979600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:209979200-209979600	Flanking Active TSS	Primary T cells from cord blood	blood

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