Variant report

Variant	rs2073487
Chromosome Location	chr1:209976646-209976647
allele	C/T
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	chr1:209975033-209981799	MCF10A-Er-Src	breast:	n/a	n/a

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
ENSG00000232222	Chromatin interaction
ENSG00000162757	Chromatin interaction
ENSG00000117595	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1005287	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1160411	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803382	0.95[YRI][hapmap]
rs12403599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015218	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs17015224	0.82[AFR][1000 genomes]
rs17015226	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs17015250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005982	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013162	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073485	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2073486	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	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235373	0.81[AFR][1000 genomes]
rs2235375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236907	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294408	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357229	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753518	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs58637469	0.82[AFR][1000 genomes]
rs59043219	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6540560	0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs6659549	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6694552	0.82[AFR][1000 genomes]
rs7545538	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550857	0.95[YRI][hapmap]
rs7552506	0.87[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs926346	0.81[AFR][1000 genomes]
rs926347	0.82[AFR][1000 genomes]
rs926348	0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2073487	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:42 , 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	chr1:209969000-209978600	Weak transcription	Lung	lung
12	chr1:209972000-209978400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:209972000-209978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:209974200-209978200	Transcr. at gene 5' and 3'	HMEC	breast
15	chr1:209974200-209978800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:209974600-209977000	Enhancers	Small Intestine	intestine
17	chr1:209974600-209977800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:209974600-209978000	Enhancers	Pancreas	Pancrea
19	chr1:209974600-209978200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:209974800-209976800	Weak transcription	Placenta	Placenta
21	chr1:209974800-209979000	Transcr. at gene 5' and 3'	NHEK	skin
22	chr1:209975000-209976800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:209975400-209977600	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr1:209975600-209977000	Enhancers	HUVEC	blood vessel
25	chr1:209975600-209977800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:209975600-209978400	Enhancers	Liver	Liver
27	chr1:209975600-209979200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:209975600-209979200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:209975800-209978200	Enhancers	Fetal Heart	heart
30	chr1:209975800-209979200	Weak transcription	Aorta	Aorta
31	chr1:209976000-209978000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:209976200-209977000	Enhancers	Gastric	stomach
33	chr1:209976200-209977000	Enhancers	Right Atrium	heart
34	chr1:209976200-209977600	Enhancers	Fetal Intestine Large	intestine
35	chr1:209976400-209976800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:209976400-209976800	Active TSS	Esophagus	oesophagus
37	chr1:209976400-209977000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:209976400-209977000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr1:209976600-209976800	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr1:209976600-209977000	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:209976600-209977600	Enhancers	Fetal Intestine Small	intestine
42	chr1:209976600-209977600	Weak transcription	Stomach Mucosa	stomach

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