Variant report

Variant	rs2073486
Chromosome Location	chr1:209976215-209976216
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	GATA2	chr1:209974681-209976222	SH-SY5Y	brain:	n/a	chr1:209975709-209975726 chr1:209975717-209975731 chr1:209975277-209975284 chr1:209975718-209975727
2	POLR2A	chr1:209975033-209981799	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr1:209973369-209976306	SK-N-SH	brain:	n/a	chr1:209974434-209974443

No.	Distal block	Cell Line	Cell type
1	chr1:209974237..209976657-chr1:209978058..209981003,3	K562	blood:
2	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
3	chr1:209974477..209976962-chr1:209977891..209979469,2	MCF-7	breast:
4	chr1:209956472..209958097-chr1:209976209..209979148,2	MCF-7	breast:

Variant related genes	Relation type
IRF6	TF binding region
ENSG00000117595	Chromatin interaction
ENSG00000232222	Chromatin interaction
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1005287	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044516	0.93[LWK][hapmap]
rs1160411	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803382	0.94[YRI][hapmap]
rs12403599	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015218	0.96[LWK][hapmap];0.86[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs17015224	0.83[AFR][1000 genomes]
rs17015226	0.93[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs17015250	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015259	0.80[JPT][hapmap]
rs2005982	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013162	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073485	1.00[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs2073487	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179254	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235372	0.86[LWK][hapmap]
rs2235373	0.82[AFR][1000 genomes]
rs2235375	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236907	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236908	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236909	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294408	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357229	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753518	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs58637469	0.83[AFR][1000 genomes]
rs59043219	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6540560	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs6659549	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685182	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6694552	0.83[AFR][1000 genomes]
rs742215	0.84[LWK][hapmap]
rs7545538	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545542	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550857	0.86[LWK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs7552506	0.93[ASW][hapmap];0.84[CEU][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs926346	0.82[AFR][1000 genomes]
rs926347	0.83[AFR][1000 genomes]
rs926348	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2073486	REN	cis	cerebellum	SCAN
rs2073486	IKBKE	cis	parietal	SCAN
rs2073486	SYT14	cis	parietal	SCAN
rs2073486	IRF6	cis	cerebellum	SCAN
rs2073486	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
4	chr1:209962200-209977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:209964200-209977800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:209964200-209978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:209964400-209978200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:209966000-209978000	Weak transcription	Colonic Mucosa	Colon
10	chr1:209966000-209978400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:209969000-209976400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:209969000-209978600	Weak transcription	Lung	lung
13	chr1:209972000-209978400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:209972000-209978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:209974000-209976400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
16	chr1:209974200-209978200	Transcr. at gene 5' and 3'	HMEC	breast
17	chr1:209974200-209978800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:209974600-209976400	Genic enhancers	Fetal Intestine Small	intestine
19	chr1:209974600-209976600	Enhancers	Stomach Mucosa	stomach
20	chr1:209974600-209977000	Enhancers	Small Intestine	intestine
21	chr1:209974600-209977800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:209974600-209978000	Enhancers	Pancreas	Pancrea
23	chr1:209974600-209978200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:209974800-209976800	Weak transcription	Placenta	Placenta
25	chr1:209974800-209979000	Transcr. at gene 5' and 3'	NHEK	skin
26	chr1:209975000-209976800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:209975400-209977600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr1:209975600-209976400	Enhancers	Left Ventricle	heart
29	chr1:209975600-209977000	Enhancers	HUVEC	blood vessel
30	chr1:209975600-209977800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:209975600-209978400	Enhancers	Liver	Liver
32	chr1:209975600-209979200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:209975600-209979200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:209975800-209978200	Enhancers	Fetal Heart	heart
35	chr1:209975800-209979200	Weak transcription	Aorta	Aorta
36	chr1:209976000-209976400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:209976000-209976400	Enhancers	Esophagus	oesophagus
38	chr1:209976000-209978000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:209976200-209976600	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr1:209976200-209976600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
41	chr1:209976200-209977000	Enhancers	Gastric	stomach
42	chr1:209976200-209977000	Enhancers	Right Atrium	heart
43	chr1:209976200-209977600	Enhancers	Fetal Intestine Large	intestine

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