Variant report

Variant	rs17317580
Chromosome Location	chr1:209987128-209987129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209980787..209983095-chr1:209985152..209988028,2	K562	blood:
2	chr1:209986954..209988866-chr1:209994555..209996958,2	K562	blood:
3	chr1:209986093..209989854-chr1:209998017..210002656,5	K562	blood:

Variant related genes	Relation type
ENSG00000117597	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	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10218448	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10489344	0.84[ASN][1000 genomes]
rs11119354	0.84[ASN][1000 genomes]
rs11582607	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584081	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11590807	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11810091	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12403006	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404886	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17389541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013196	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601717	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34743335	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753510	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753513	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766615	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41274838	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240837	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56071308	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56268268	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61820635	0.84[ASN][1000 genomes]
rs6699507	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72741048	0.89[EUR][1000 genomes]
rs7526313	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544804	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546104	0.84[ASN][1000 genomes]
rs932334	0.86[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
rs17317580	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209979800-209989200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:209981800-209989200	Weak transcription	Esophagus	oesophagus
3	chr1:209981800-209989600	Weak transcription	Spleen	Spleen
4	chr1:209981800-209989800	Weak transcription	Right Atrium	heart
5	chr1:209982000-209989200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:209982400-209989200	Weak transcription	Placenta	Placenta
7	chr1:209984200-209988000	Weak transcription	Fetal Thymus	thymus
8	chr1:209984400-209987800	Weak transcription	NHEK	skin
9	chr1:209984400-209988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:209984400-209989200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:209984600-209987800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:209984600-209988200	Weak transcription	K562	blood
13	chr1:209985400-209989200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:209985600-209987800	Weak transcription	HMEC	breast
15	chr1:209985800-209987800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:209986800-209988200	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links