Variant report

Variant	rs2013196
Chromosome Location	chr1:209968411-209968412
allele	C/T
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	STAT3	chr1:209968395-209968422	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209967414..209971362-chr1:209996696..210001970,5	MCF-7	breast:
2	chr1:209963000..209964602-chr1:209967269..209969654,2	K562	blood:

Variant related genes	Relation type
IRF6	TF binding region
ENSG00000117597	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10127937	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10218448	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10489344	1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs11119344	0.84[CEU][hapmap]
rs11119354	1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs11582607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584081	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11590807	1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11810091	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12403006	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17317580	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17389541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601717	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34743335	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753510	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753513	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766615	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41274838	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240837	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56071308	0.88[ASN][1000 genomes]
rs56268268	0.89[ASN][1000 genomes]
rs61820635	0.84[ASN][1000 genomes]
rs6699507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72741048	0.84[EUR][1000 genomes]
rs7526313	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544804	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546104	0.84[ASN][1000 genomes]
rs932334	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1067914	chr1:209955818-209972979	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2013196	IRF6	cis	cerebellum	SCAN
rs2013196	IRF6	cis	Whole Blood	GTEx
rs2013196	IKBKE	cis	parietal	SCAN
rs2013196	HHAT	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958000-209971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209958400-209968600	Weak transcription	Lung	lung
4	chr1:209958400-209971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
6	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:209958600-209971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:209958600-209972000	Weak transcription	Fetal Kidney	kidney
9	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
10	chr1:209960800-209969000	Strong transcription	Placenta	Placenta
11	chr1:209961000-209974600	Weak transcription	Right Atrium	heart
12	chr1:209961600-209974600	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr1:209962000-209972600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:209962200-209977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:209964200-209976000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:209964200-209977800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:209964200-209978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:209964400-209978200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:209964600-209971600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:209965200-209975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:209965600-209969600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:209965800-209970600	Strong transcription	Liver	Liver
24	chr1:209965800-209974600	Weak transcription	Small Intestine	intestine
25	chr1:209966000-209969400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:209966000-209973000	Weak transcription	Left Ventricle	heart
27	chr1:209966000-209976200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:209966000-209978000	Weak transcription	Colonic Mucosa	Colon
29	chr1:209966000-209978400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:209966200-209968600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:209966200-209970800	Weak transcription	Stomach Mucosa	stomach
32	chr1:209966200-209974600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr1:209966400-209971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:209966400-209971200	Strong transcription	HMEC	breast
35	chr1:209966600-209968600	Strong transcription	Fetal Intestine Large	intestine
36	chr1:209967000-209968800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:209967000-209969600	Strong transcription	Pancreas	Pancrea
38	chr1:209968000-209968800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:209968000-209968800	Genic enhancers	NHEK	skin
40	chr1:209968000-209970000	Strong transcription	HUVEC	blood vessel
41	chr1:209968000-209972000	Genic enhancers	Fetal Intestine Small	intestine
42	chr1:209968400-209969000	Strong transcription	Gastric	stomach
43	chr1:209968400-209969000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:209968400-209969600	Strong transcription	Esophagus	oesophagus
45	chr1:209968400-209971200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:209968400-209971800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:209968400-209975000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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