Variant report

Variant	rs17015250
Chromosome Location	chr1:209978777-209978778
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:209978720-209978870	HMEC	breast:	n/a	n/a
2	RAD21	chr1:209978691-209979166	H1-hESC	embryonic stem cell:	n/a	chr1:209979026-209979038
3	CTCF	chr1:209978680-209978830	HEEpiC	esophagus:	n/a	n/a
4	POLR2A	chr1:209978698-209980017	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr1:209978760-209978910	HEEpiC	esophagus:	n/a	n/a
6	CTCF	chr1:209978732-209979170	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:209978258-209980648	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:209975033-209981799	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:209978772-209979892	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr1:209978717-209979907	H1-hESC	embryonic stem cell:	n/a	chr1:209979611-209979624
11	CTCF	chr1:209978661-209978797	NHEK	skin:	n/a	n/a
12	CTCF	chr1:209978720-209978870	RPTEC	kidney:	n/a	n/a
13	TBP	chr1:209978754-209979977	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:209978560-209980111	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr1:209978727-209979982	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr1:209978660-209978810	NHEK	skin:	n/a	n/a
17	CTCF	chr1:209978755-209979148	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr1:209978660-209978810	SAEC	small airway:	n/a	n/a

No data

(count:8 , 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	chr1:209977871..209981214-chr1:209999703..210002866,6	K562	blood:
7	chr1:209974237..209976657-chr1:209978058..209981003,3	K562	blood:
8	chr1:209956472..209958097-chr1:209976209..209979148,2	MCF-7	breast:

No data

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

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1005287	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1160411	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12403599	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]
rs17015218	0.83[MKK][hapmap]
rs17015226	0.83[MKK][hapmap]
rs2005982	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013162	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073485	0.83[MKK][hapmap]
rs2073486	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179254	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236907	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294408	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357229	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59043219	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6659549	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545538	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545542	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]
rs7552506	0.88[CEU][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs926348	0.93[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17015250	SYT14	cis	parietal	SCAN
rs17015250	REN	cis	cerebellum	SCAN
rs17015250	IKBKE	cis	parietal	SCAN
rs17015250	IRF6	cis	cerebellum	SCAN
rs17015250	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
2	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:209974200-209978800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:209974800-209979000	Transcr. at gene 5' and 3'	NHEK	skin
5	chr1:209975600-209979200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:209975600-209979200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:209975800-209979200	Weak transcription	Aorta	Aorta
8	chr1:209977000-209980000	Active TSS	Esophagus	oesophagus
9	chr1:209977400-209979800	Active TSS	Duodenum Mucosa	Duodenum
10	chr1:209977600-209979400	Weak transcription	HSMMtube	muscle
11	chr1:209977600-209980200	Flanking Active TSS	HUVEC	blood vessel
12	chr1:209977800-209979200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:209977800-209979200	Bivalent/Poised TSS	Fetal Thymus	thymus
14	chr1:209977800-209979400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr1:209977800-209979600	Active TSS	Fetal Intestine Large	intestine
16	chr1:209977800-209979600	Active TSS	Gastric	stomach
17	chr1:209977800-209980000	Active TSS	Rectal Smooth Muscle	rectum
18	chr1:209977800-209980200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:209978000-209979000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:209978000-209979200	Bivalent/Poised TSS	Fetal Stomach	stomach
21	chr1:209978000-209979200	Active TSS	Thymus	Thymus
22	chr1:209978000-209979400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:209978000-209979600	Active TSS	Fetal Intestine Small	intestine
24	chr1:209978000-209980400	Active TSS	Colonic Mucosa	Colon
25	chr1:209978200-209978800	Flanking Active TSS	Fetal Heart	heart
26	chr1:209978200-209979800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr1:209978200-209980200	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:209978200-209980400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:209978200-209980400	Active TSS	HMEC	breast
30	chr1:209978400-209979000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr1:209978400-209979000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:209978400-209979200	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr1:209978400-209979200	Active TSS	Stomach Smooth Muscle	stomach
34	chr1:209978400-209979400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr1:209978400-209979400	Active TSS	Placenta Amnion	Placenta Amnion
36	chr1:209978400-209979600	Active TSS	Stomach Mucosa	stomach
37	chr1:209978400-209979800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr1:209978400-209979800	Active TSS	Fetal Kidney	kidney
39	chr1:209978400-209980000	Active TSS	H1 Cell Line	embryonic stem cell
40	chr1:209978400-209980000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr1:209978400-209980000	Flanking Active TSS	Liver	Liver
42	chr1:209978600-209978800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:209978600-209978800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:209978600-209978800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
45	chr1:209978600-209978800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:209978600-209978800	Enhancers	Spleen	Spleen
47	chr1:209978600-209979000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:209978600-209979000	Active TSS	Placenta	Placenta
49	chr1:209978600-209979000	Active TSS	Right Atrium	heart
50	chr1:209978600-209979200	Active TSS	Lung	lung

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