Variant report

Variant	rs6659549
Chromosome Location	chr1:209980155-209980156
allele	G/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	IRF1	chr1:209979475-209980173	K562	blood:	n/a	chr1:209979523-209979537 chr1:209980083-209980097 chr1:209980081-209980091 chr1:209980081-209980095 chr1:209979542-209979556
2	POLR2A	chr1:209978258-209980648	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF384	chr1:209980041-209980467	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:209975033-209981799	MCF10A-Er-Src	breast:	n/a	n/a
5	NR2F2	chr1:209979363-209980246	K562	blood:	n/a	n/a
6	IRF1	chr1:209979490-209980180	K562	blood:	n/a	chr1:209979523-209979537 chr1:209980083-209980097 chr1:209980081-209980091 chr1:209980081-209980095 chr1:209979542-209979556
7	ZNF384	chr1:209979331-209981763	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209979052..209983681-chr1:210545344..210549112,5	K562	blood:
2	chr1:209977871..209984485-chr1:209998424..210002427,6	K562	blood:
3	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
4	chr1:209979695..209981280-chr1:209983415..209985096,2	K562	blood:
5	chr1:209956289..209959543-chr1:209978892..209981541,4	K562	blood:
6	chr1:209979780..209981458-chr1:209981509..209984915,3	K562	blood:
7	chr1:209968649..209970778-chr1:209979506..209982286,2	K562	blood:
8	chr1:209977871..209981214-chr1:209999703..210002866,6	K562	blood:
9	chr1:209974237..209976657-chr1:209978058..209981003,3	K562	blood:

Variant related genes	Relation type
IRF6	TF binding region
ENSG00000200972	Chromatin interaction
ENSG00000232222	Chromatin interaction
ENSG00000117595	Chromatin interaction
ENSG00000117597	Chromatin interaction
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1005287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1160411	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803382	0.81[AFR][1000 genomes]
rs11805830	0.81[AFR][1000 genomes]
rs12403599	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015250	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005982	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013162	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073486	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073487	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179254	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235375	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236907	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236908	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236909	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294408	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753518	0.81[AFR][1000 genomes]
rs59043219	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6540560	0.83[AFR][1000 genomes]
rs6685182	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545538	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552506	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs926348	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[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
rs6659549	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209977600-209980200	Flanking Active TSS	HUVEC	blood vessel
2	chr1:209977800-209980200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:209978000-209980400	Active TSS	Colonic Mucosa	Colon
4	chr1:209978200-209980200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:209978200-209980400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:209978200-209980400	Active TSS	HMEC	breast
7	chr1:209979000-209980400	Active TSS	NHEK	skin
8	chr1:209979200-209980200	Flanking Active TSS	K562	blood
9	chr1:209979400-209980200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:209979400-209980400	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:209979600-209980800	Weak transcription	HSMMtube	muscle
12	chr1:209979600-209985000	Weak transcription	Gastric	stomach
13	chr1:209979800-209980200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:209979800-209980200	Active TSS	Primary B cells from cord blood	blood
15	chr1:209979800-209980600	Enhancers	Placenta	Placenta
16	chr1:209979800-209980800	Weak transcription	Right Ventricle	heart
17	chr1:209979800-209981400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:209979800-209981400	Weak transcription	Spleen	Spleen
19	chr1:209979800-209989200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:209980000-209980200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:209980000-209980200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:209980000-209980200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:209980000-209980200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:209980000-209980200	Active TSS	Duodenum Mucosa	Duodenum
25	chr1:209980000-209980200	Weak transcription	Small Intestine	intestine
26	chr1:209980000-209980200	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr1:209980000-209980200	Enhancers	NH-A	brain
28	chr1:209980000-209980200	Enhancers	NHLF	lung
29	chr1:209980000-209980200	Enhancers	Osteobl	bone
30	chr1:209980000-209980400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:209980000-209980400	Enhancers	Stomach Smooth Muscle	stomach
32	chr1:209980000-209980600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:209980000-209980800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:209980000-209980800	Weak transcription	Pancreas	Pancrea
35	chr1:209980000-209980800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:209980000-209981000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:209980000-209981000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:209980000-209981000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:209980000-209981000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:209980000-209981000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:209980000-209981000	Enhancers	Fetal Heart	heart
42	chr1:209980000-209981000	Weak transcription	NHDF-Ad	bronchial
43	chr1:209980000-209981400	Weak transcription	Esophagus	oesophagus
44	chr1:209980000-209981400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:209980000-209981600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:209980000-209981600	Weak transcription	Adipose Nuclei	Adipose
47	chr1:209980000-209981600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:209980000-209981600	Weak transcription	Right Atrium	heart
49	chr1:209980000-209982000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:209980000-209982000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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