Variant report

Variant	rs59043219
Chromosome Location	chr1:209970610-209970611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209970042..209972449-chr1:209978125..209979735,2	K562	blood:
2	chr1:209961943..209965694-chr1:209969094..209971510,3	K562	blood:
3	chr1:209968649..209970778-chr1:209979506..209982286,2	K562	blood:
4	chr1:209957462..209959935-chr1:209968588..209972462,3	K562	blood:
5	chr1:209969439..209971872-chr1:209988283..209991092,2	MCF-7	breast:
6	chr1:209967414..209971362-chr1:209996696..210001970,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162757	Chromatin interaction
ENSG00000117597	Chromatin interaction
ENSG00000117595	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1005287	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1160411	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12403599	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17015250	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2005982	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013162	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2073485	0.81[AFR][1000 genomes]
rs2073486	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2073487	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2179254	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2235375	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2236907	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2236908	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2236909	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2294408	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2357229	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6659549	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6685182	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7545538	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7545542	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7552506	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs926348	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59043219	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:48 , 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	chr1:209958400-209971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
5	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:209958600-209971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:209958600-209972000	Weak transcription	Fetal Kidney	kidney
8	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
9	chr1:209961000-209974600	Weak transcription	Right Atrium	heart
10	chr1:209961600-209974600	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr1:209962000-209972600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:209962200-209977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:209964200-209976000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:209964200-209977800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:209964200-209978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:209964400-209978200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:209964600-209971600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:209965200-209975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:209965800-209974600	Weak transcription	Small Intestine	intestine
21	chr1:209966000-209973000	Weak transcription	Left Ventricle	heart
22	chr1:209966000-209976200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:209966000-209978000	Weak transcription	Colonic Mucosa	Colon
24	chr1:209966000-209978400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:209966200-209970800	Weak transcription	Stomach Mucosa	stomach
26	chr1:209966200-209974600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr1:209966400-209971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:209966400-209971200	Strong transcription	HMEC	breast
29	chr1:209968000-209972000	Genic enhancers	Fetal Intestine Small	intestine
30	chr1:209968400-209971200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:209968400-209971800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:209968400-209975000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:209968600-209974200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:209968800-209971000	Strong transcription	NHEK	skin
35	chr1:209968800-209971600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:209968800-209974600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:209969000-209971000	Enhancers	Fetal Intestine Large	intestine
38	chr1:209969000-209971400	Weak transcription	Gastric	stomach
39	chr1:209969000-209972600	Weak transcription	Placenta	Placenta
40	chr1:209969000-209976400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:209969000-209978600	Weak transcription	Lung	lung
42	chr1:209969400-209971400	Genic enhancers	Duodenum Mucosa	Duodenum
43	chr1:209969600-209971000	Genic enhancers	Esophagus	oesophagus
44	chr1:209970000-209971000	Weak transcription	Pancreas	Pancrea
45	chr1:209970000-209973200	Weak transcription	HUVEC	blood vessel
46	chr1:209970000-209975400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:209970600-209971000	Weak transcription	Fetal Heart	heart
48	chr1:209970600-209972800	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links