Variant report

Variant	rs724286
Chromosome Location	chr1:210036699-210036700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210034979..210037357-chr1:210546049..210549012,2	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11119356	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12401430	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12410900	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56254710	0.94[EUR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs724286	IRF6	cis	Whole Blood	GTEx
rs724286	IKBKE	cis	parietal	SCAN
rs724286	IRF6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210017600-210041200	Weak transcription	Fetal Brain Male	brain
2	chr1:210027600-210036800	Weak transcription	HSMM	muscle
3	chr1:210028200-210042400	Weak transcription	NHDF-Ad	bronchial
4	chr1:210028400-210036800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:210028400-210037400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:210028400-210039600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:210028800-210036800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:210029600-210037400	Weak transcription	Lung	lung
9	chr1:210034000-210037600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:210034200-210037400	Enhancers	Brain Hippocampus Middle	brain
11	chr1:210034200-210037600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:210034200-210037600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:210034200-210038600	Enhancers	HMEC	breast
14	chr1:210034400-210037200	Enhancers	Brain Angular Gyrus	brain
15	chr1:210034600-210037000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:210035000-210037600	Enhancers	Brain Cingulate Gyrus	brain
17	chr1:210035400-210038000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:210035400-210038000	Enhancers	H9 Cell Line	embryonic stem cell
19	chr1:210035400-210038000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:210035600-210036800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr1:210035600-210036800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr1:210035600-210037600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:210035800-210037600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:210035800-210037600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:210035800-210037600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr1:210035800-210038000	Enhancers	Brain Anterior Caudate	brain
27	chr1:210036000-210036800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr1:210036000-210038000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:210036200-210037400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:210036200-210037400	Enhancers	Fetal Lung	lung
31	chr1:210036200-210037600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:210036200-210037600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:210036200-210037600	Enhancers	HSMMtube	muscle
34	chr1:210036200-210038000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:210036200-210038600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:210036400-210036800	Enhancers	Fetal Muscle Leg	muscle
37	chr1:210036400-210036800	Enhancers	Ovary	ovary
38	chr1:210036400-210037200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:210036400-210037400	Enhancers	Hela-S3	cervix
40	chr1:210036400-210037800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:210036400-210038000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:210036400-210038000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr1:210036400-210038600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr1:210036400-210038600	Enhancers	NHEK	skin
45	chr1:210036600-210036800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr1:210036600-210037000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:210036600-210037200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:210036600-210037200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr1:210036600-210037400	Enhancers	Brain Germinal Matrix	brain

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