Variant report

Variant	rs932334
Chromosome Location	chr1:209996896-209996897
allele	C/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	POLR2A	chr1:209996758-209997377	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr1:209996871-209996978	GM13977	blood:	n/a	n/a
3	FOS	chr1:209996489-209997254	MCF10A-Er-Src	breast:	n/a	chr1:209997150-209997161
4	JUN	chr1:209996522-209997354	HUVEC	blood vessel:	n/a	chr1:209997150-209997161
5	RAD21	chr1:209995813-209997481	SK-N-SH	brain:	n/a	chr1:209996621-209996628 chr1:209996619-209996638
6	GABPA	chr1:209996363-209997306	SK-N-SH	brain:	n/a	n/a
7	KAP1	chr1:209996347-209997258	U2OS	brain:	n/a	n/a
8	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
9	CTCF	chr1:209995894-209997087	A549	lung:	n/a	chr1:209996621-209996634 chr1:209996618-209996636 chr1:209996620-209996641 chr1:209996623-209996631 chr1:209996619-209996635
10	CTCF	chr1:209996411-209996911	HCT-116	colon:	n/a	chr1:209996621-209996634 chr1:209996618-209996636 chr1:209996620-209996641 chr1:209996623-209996631 chr1:209996619-209996635
11	STAT3	chr1:209996876-209997213	MCF10A-Er-Src	breast:	n/a	n/a
12	FOXA1	chr1:209996894-209997604	T-47D	breast:	n/a	n/a
13	CTCF	chr1:209996880-209997030	GM12871	blood:	n/a	n/a
14	SMC3	chr1:209996030-209997607	SK-N-SH	brain:	n/a	chr1:209996620-209996634
15	RAD21	chr1:209996415-209996907	IMR90	lung:	n/a	chr1:209996621-209996628 chr1:209996619-209996638
16	POLR2A	chr1:209996790-209997382	SK-N-SH	brain:	n/a	n/a
17	CTCF	chr1:209996760-209996910	NHEK	skin:	n/a	n/a
18	MYC	chr1:209996496-209997151	MCF10A-Er-Src	breast:	n/a	n/a
19	CTCF	chr1:209996393-209996909	K562	blood:	n/a	chr1:209996621-209996634 chr1:209996618-209996636 chr1:209996620-209996641 chr1:209996623-209996631 chr1:209996619-209996635
20	CTCF	chr1:209996880-209997030	NHDF-neo	bronchial:	n/a	n/a
21	RAD21	chr1:209996306-209996984	HCT-116	colon:	n/a	chr1:209996621-209996628 chr1:209996619-209996638
22	GATA3	chr1:209996784-209997484	T-47D	breast:	n/a	n/a
23	FOS	chr1:209996561-209997258	MCF10A-Er-Src	breast:	n/a	chr1:209997150-209997161
24	GATA2	chr1:209996363-209997460	HUVEC	blood vessel:	n/a	n/a
25	FOS	chr1:209996221-209997426	HUVEC	blood vessel:	n/a	chr1:209997150-209997161
26	GATA3	chr1:209996390-209997475	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr1:209996382-209997360	HUVEC	blood vessel:	n/a	n/a
28	TAF1	chr1:209996468-209997167	PFSK-1	brain:	n/a	n/a
29	TCF12	chr1:209996324-209997537	SK-N-SH	brain:	n/a	n/a
30	STAT3	chr1:209996891-209997174	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr1:209996226-209997493	HUVEC	blood vessel:	n/a	n/a
32	CTCF	chr1:209996760-209996910	HUVEC	blood vessel:	n/a	n/a
33	FOSL2	chr1:209996374-209997424	SK-N-SH	brain:	n/a	chr1:209997150-209997161
34	GATA3	chr1:209996357-209997569	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr1:209996344-209997381	HUVEC	blood vessel:	n/a	n/a
36	TCF12	chr1:209996434-209997433	SK-N-SH	brain:	n/a	n/a
37	BRCA1	chr1:209996880-209996902	GM12878	blood:	n/a	n/a
38	CTCF	chr1:209996282-209997006	IMR90	lung:	n/a	chr1:209996621-209996634 chr1:209996618-209996636 chr1:209996620-209996641 chr1:209996623-209996631 chr1:209996619-209996635
39	POLR2A	chr1:209996533-209997213	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr1:209996786-209997244	HUVEC	blood vessel:	n/a	n/a
41	NFIC	chr1:209996319-209997350	SK-N-SH	brain:	n/a	n/a
42	CTCF	chr1:209996880-209997030	HCM	heart:	n/a	n/a
43	SMC3	chr1:209996426-209997195	Hela-S3	cervix:	n/a	chr1:209996620-209996634
44	RAD21	chr1:209996369-209996931	HCT-116	colon:	n/a	chr1:209996621-209996628 chr1:209996619-209996638
45	ZNF143	chr1:209996399-209997125	K562	blood:	n/a	n/a
46	STAT3	chr1:209996685-209997212	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr1:209996799-209997200	MCF10A-Er-Src	breast:	n/a	chr1:209997150-209997161
48	MYC	chr1:209996463-209997285	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr1:209996060-209997747	HUVEC	blood vessel:	n/a	n/a
50	GATA3	chr1:209996842-209997431	T-47D	breast:	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	chr1:209986954..209988866-chr1:209994555..209996958,2	K562	blood:
4	chr1:209981459..209983151-chr1:209995817..209998034,2	MCF-7	breast:
5	chr1:209956403..209959682-chr1:209995169..209998983,4	K562	blood:
6	chr1:209974442..209977095-chr1:209996452..209999044,2	MCF-7	breast:
7	chr1:209995353..209998573-chr1:209998823..210001196,6	K562	blood:
8	chr1:209984333..209986966-chr1:209996753..209999573,2	MCF-7	breast:
9	chr1:209991265..209992886-chr1:209994565..209997143,2	MCF-7	breast:
10	chr1:209984299..209986962-chr1:209994291..209996939,2	MCF-7	breast:
11	chr1:209977911..209983292-chr1:209996386..210001078,7	MCF-7	breast:
12	chr1:209981422..209983543-chr1:209995395..209998153,2	K562	blood:

Variant related genes	Relation type
DIEXF	TF binding region
ENSG00000117597	Chromatin interaction
ENSG00000162757	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10218448	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489344	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119354	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582607	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11584081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590807	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11810091	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401430	0.86[ASN][1000 genomes]
rs12403006	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12404886	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17317580	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17389541	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013196	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28601717	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743335	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753510	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753513	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766615	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41274838	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240837	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071308	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268268	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61820635	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699507	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72741048	0.84[AFR][1000 genomes]
rs7526313	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544804	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546104	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[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
rs932334	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:50 , 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	chr1:209996000-209997000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:209996000-209997000	Enhancers	Fetal Heart	heart
6	chr1:209996000-209997000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:209996000-209997000	Enhancers	Dnd41	blood
8	chr1:209996000-209997200	Enhancers	HSMM	muscle
9	chr1:209996000-209997400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:209996000-209997400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:209996000-209997600	Flanking Active TSS	NHEK	skin
12	chr1:209996000-210000800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:209996200-209997000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:209996200-209997000	Weak transcription	Gastric	stomach
15	chr1:209996200-209997000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr1:209996200-209997000	Enhancers	HepG2	liver
17	chr1:209996200-209997200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:209996200-209997200	Enhancers	Hela-S3	cervix
19	chr1:209996200-209997400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:209996200-209997400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:209996200-209997400	Flanking Active TSS	HUVEC	blood vessel
22	chr1:209996200-209997400	Flanking Active TSS	Osteobl	bone
23	chr1:209996200-209997600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:209996400-209997000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:209996400-209997000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr1:209996400-209997000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:209996400-209997000	Enhancers	Brain Hippocampus Middle	brain
28	chr1:209996400-209997000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
29	chr1:209996400-209997200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:209996400-209998800	Weak transcription	Fetal Intestine Large	intestine
31	chr1:209996600-209997000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:209996600-209997000	Flanking Active TSS	NHDF-Ad	bronchial
33	chr1:209996600-209997200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:209996600-209997200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:209996600-209997200	Active TSS	Brain Anterior Caudate	brain
36	chr1:209996600-209997200	Active TSS	A549	lung
37	chr1:209996600-209997200	Enhancers	K562	blood
38	chr1:209996600-209999200	Weak transcription	HSMMtube	muscle
39	chr1:209996600-210000400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:209996600-210000800	Weak transcription	Liver	Liver
41	chr1:209996600-210000800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:209996600-210000800	Enhancers	HMEC	breast
43	chr1:209996800-209997000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:209996800-209997000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:209996800-209997000	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr1:209996800-209997200	Flanking Active TSS	NH-A	brain
47	chr1:209996800-209997400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr1:209996800-210000600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:209996800-210000800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:209996800-210000800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links