Variant report

Variant	rs12403599
Chromosome Location	chr1:209979014-209979015
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

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	CTCF	chr1:209978920-209979070	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:209978894-209979130	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr1:209978691-209979166	H1-hESC	embryonic stem cell:	n/a	chr1:209979026-209979038
5	POLR2A	chr1:209978698-209980017	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:209978880-209979030	HBMEC	blood vessel:	n/a	n/a
7	CTCF	chr1:209978732-209979170	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr1:209978930-209979043	NHEK	skin:	n/a	n/a
9	CTCF	chr1:209978931-209979017	LNCaP	prostate:	n/a	n/a
10	POLR2A	chr1:209978258-209980648	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:209975033-209981799	MCF10A-Er-Src	breast:	n/a	n/a
12	CTCF	chr1:209978920-209979070	Caco-2	colon:	n/a	n/a
13	POLR2A	chr1:209978772-209979892	H1-hESC	embryonic stem cell:	n/a	n/a
14	CHD2	chr1:209978903-209979922	H1-hESC	embryonic stem cell:	n/a	chr1:209979487-209979497
15	MXI1	chr1:209978850-209979795	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr1:209978880-209979030	HRE	kidney:	n/a	n/a
17	CTCF	chr1:209978960-209979110	RPTEC	kidney:	n/a	n/a
18	SIN3A	chr1:209978717-209979907	H1-hESC	embryonic stem cell:	n/a	chr1:209979611-209979624
19	MAX	chr1:209978902-209979882	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr1:209978920-209979070	HEK293	kidney:	n/a	n/a
21	TBP	chr1:209978754-209979977	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:209978560-209980111	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF1	chr1:209978727-209979982	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr1:209978850-209979059	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr1:209978836-209979072	H1-hESC	embryonic stem cell:	n/a	chr1:209979026-209979038
26	JUND	chr1:209978962-209979971	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr1:209978755-209979148	H1-hESC	embryonic stem cell:	n/a	n/a
28	BACH1	chr1:209978779-209979894	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:209976817..209979056-chr1:209982865..209985197,2	K562	blood:
2	chr1:209977687..209979481-chr1:210546829..210548447,2	MCF-7	breast:
3	chr1:209974477..209976962-chr1:209977891..209979469,2	MCF-7	breast:
4	chr1:209977871..209984485-chr1:209998424..210002427,6	K562	blood:
5	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
6	chr1:209956289..209959543-chr1:209978892..209981541,4	K562	blood:
7	chr1:209977871..209981214-chr1:209999703..210002866,6	K562	blood:
8	chr1:209974237..209976657-chr1:209978058..209981003,3	K562	blood:
9	chr1:209956472..209958097-chr1:209976209..209979148,2	MCF-7	breast:

No data

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

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1005287	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1160411	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803382	0.95[YRI][hapmap]
rs17015218	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs17015224	0.82[AFR][1000 genomes]
rs17015226	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs17015250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005982	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013162	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073485	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2073486	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179254	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235373	0.81[AFR][1000 genomes]
rs2235375	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236907	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236908	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294408	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357229	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753518	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs58637469	0.82[AFR][1000 genomes]
rs59043219	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6540560	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs6659549	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685182	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6694552	0.82[AFR][1000 genomes]
rs7545538	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545542	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]
rs7550857	0.95[YRI][hapmap]
rs7552506	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs926346	0.81[AFR][1000 genomes]
rs926347	0.82[AFR][1000 genomes]
rs926348	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12403599	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209975600-209979200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:209975600-209979200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:209975800-209979200	Weak transcription	Aorta	Aorta
4	chr1:209977000-209980000	Active TSS	Esophagus	oesophagus
5	chr1:209977400-209979800	Active TSS	Duodenum Mucosa	Duodenum
6	chr1:209977600-209979400	Weak transcription	HSMMtube	muscle
7	chr1:209977600-209980200	Flanking Active TSS	HUVEC	blood vessel
8	chr1:209977800-209979200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:209977800-209979200	Bivalent/Poised TSS	Fetal Thymus	thymus
10	chr1:209977800-209979400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr1:209977800-209979600	Active TSS	Fetal Intestine Large	intestine
12	chr1:209977800-209979600	Active TSS	Gastric	stomach
13	chr1:209977800-209980000	Active TSS	Rectal Smooth Muscle	rectum
14	chr1:209977800-209980200	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:209978000-209979200	Bivalent/Poised TSS	Fetal Stomach	stomach
16	chr1:209978000-209979200	Active TSS	Thymus	Thymus
17	chr1:209978000-209979400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:209978000-209979600	Active TSS	Fetal Intestine Small	intestine
19	chr1:209978000-209980400	Active TSS	Colonic Mucosa	Colon
20	chr1:209978200-209979800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr1:209978200-209980200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr1:209978200-209980400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:209978200-209980400	Active TSS	HMEC	breast
24	chr1:209978400-209979200	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr1:209978400-209979200	Active TSS	Stomach Smooth Muscle	stomach
26	chr1:209978400-209979400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr1:209978400-209979400	Active TSS	Placenta Amnion	Placenta Amnion
28	chr1:209978400-209979600	Active TSS	Stomach Mucosa	stomach
29	chr1:209978400-209979800	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:209978400-209979800	Active TSS	Fetal Kidney	kidney
31	chr1:209978400-209980000	Active TSS	H1 Cell Line	embryonic stem cell
32	chr1:209978400-209980000	Active TSS	H9 Cell Line	embryonic stem cell
33	chr1:209978400-209980000	Flanking Active TSS	Liver	Liver
34	chr1:209978600-209979200	Active TSS	Lung	lung
35	chr1:209978600-209979400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr1:209978600-209979400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr1:209978600-209979600	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr1:209978600-209979600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:209978600-209979600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr1:209978600-209979800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:209978600-209979800	Active TSS	Pancreas	Pancrea
42	chr1:209978600-209979800	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr1:209978600-209980000	Active TSS	Small Intestine	intestine
44	chr1:209978800-209979200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
45	chr1:209978800-209979200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:209978800-209979200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:209978800-209979200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr1:209978800-209979200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:209978800-209979200	Active TSS	Fetal Heart	heart
50	chr1:209978800-209979200	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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