Variant report

Variant	rs11584081
Chromosome Location	chr1:209997448-209997449
allele	A/G
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	USF2	chr1:209997174-209997619	K562	blood:	n/a	n/a
2	RAD21	chr1:209995813-209997481	SK-N-SH	brain:	n/a	chr1:209996621-209996628 chr1:209996619-209996638
3	CTCF	chr1:209995795-209997524	SK-N-SH	brain:	n/a	chr1:209996621-209996634 chr1:209996618-209996636 chr1:209996620-209996641 chr1:209996623-209996631 chr1:209996619-209996635
4	FOXA1	chr1:209996894-209997604	T-47D	breast:	n/a	n/a
5	SMC3	chr1:209996030-209997607	SK-N-SH	brain:	n/a	chr1:209996620-209996634
6	GATA3	chr1:209996784-209997484	T-47D	breast:	n/a	n/a
7	GATA2	chr1:209996363-209997460	HUVEC	blood vessel:	n/a	n/a
8	GATA3	chr1:209996390-209997475	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr1:209996324-209997537	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr1:209996226-209997493	HUVEC	blood vessel:	n/a	n/a
11	GATA3	chr1:209996357-209997569	SK-N-SH	brain:	n/a	n/a
12	FOXA1	chr1:209997131-209997635	T-47D	breast:	n/a	n/a
13	POLR2A	chr1:209996060-209997747	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209994924..209998418-chr1:209998758..210004178,10	K562	blood:
2	chr1:209977270..209980591-chr1:209996227..209999228,3	MCF-7	breast:
3	chr1:209981459..209983151-chr1:209995817..209998034,2	MCF-7	breast:
4	chr1:209956403..209959682-chr1:209995169..209998983,4	K562	blood:
5	chr1:209974442..209977095-chr1:209996452..209999044,2	MCF-7	breast:
6	chr1:209995353..209998573-chr1:209998823..210001196,6	K562	blood:
7	chr1:209984333..209986966-chr1:209996753..209999573,2	MCF-7	breast:
8	chr1:209991325..209994197-chr1:209997349..210000501,3	K562	blood:
9	chr1:209977911..209983292-chr1:209996386..210001078,7	MCF-7	breast:
10	chr1:209997233..209999615-chr1:210545507..210547637,2	MCF-7	breast:
11	chr1:209981422..209983543-chr1:209995395..209998153,2	K562	blood:

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

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10127937	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10218448	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489344	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119354	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582607	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11590807	0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11810091	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401430	0.86[ASN][1000 genomes]
rs12403006	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12404886	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17317580	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17389541	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013196	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28601717	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743335	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753510	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753513	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766615	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41274838	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240837	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071308	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268268	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61820635	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699507	0.88[JPT][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72741048	0.84[AFR][1000 genomes]
rs7526313	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544804	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546104	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs11584081	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209992600-210000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:209993400-209999000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:209995800-209998000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:209996000-209997600	Flanking Active TSS	NHEK	skin
5	chr1:209996000-210000800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:209996200-209997600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:209996400-209998800	Weak transcription	Fetal Intestine Large	intestine
8	chr1:209996600-209999200	Weak transcription	HSMMtube	muscle
9	chr1:209996600-210000400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:209996600-210000800	Weak transcription	Liver	Liver
11	chr1:209996600-210000800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:209996600-210000800	Enhancers	HMEC	breast
13	chr1:209996800-210000600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:209996800-210000800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:209996800-210000800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:209997000-209997800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr1:209997000-209999200	Weak transcription	HepG2	liver
18	chr1:209997000-210000000	Weak transcription	Dnd41	blood
19	chr1:209997000-210000600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:209997000-210000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:209997000-210000800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:209997000-210000800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:209997000-210000800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:209997000-210000800	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:209997000-210000800	Weak transcription	Fetal Heart	heart
26	chr1:209997200-209998800	Weak transcription	K562	blood
27	chr1:209997200-209999400	Weak transcription	A549	lung
28	chr1:209997200-210000800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:209997200-210000800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:209997200-210000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:209997200-210000800	Weak transcription	Hela-S3	cervix
32	chr1:209997200-210000800	Weak transcription	HSMM	muscle
33	chr1:209997200-210001000	Weak transcription	Gastric	stomach
34	chr1:209997400-209997600	Enhancers	Osteobl	bone
35	chr1:209997400-209998400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:209997400-209998600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:209997400-209999400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:209997400-209999600	Enhancers	HUVEC	blood vessel
39	chr1:209997400-210000600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:209997400-210000800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:209997400-210000800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:209997400-210000800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:209997400-210000800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:209997400-210000800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:209997400-210000800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:209997400-210000800	Weak transcription	Adipose Nuclei	Adipose
47	chr1:209997400-210000800	Weak transcription	Left Ventricle	heart
48	chr1:209997400-210000800	Weak transcription	NH-A	brain
49	chr1:209997400-210000800	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links