Variant report

Variant	rs28601717
Chromosome Location	chr1:210000390-210000391
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	GATA1	chr1:209999983-210001849	K562	blood:	n/a	chr1:210001706-210001716
2	GTF3C2	chr1:210000384-210001847	K562	blood:	n/a	n/a
3	RCOR1	chr1:210000243-210001790	K562	blood:	n/a	n/a
4	MYC	chr1:210000279-210001869	K562	blood:	n/a	chr1:210001329-210001338 chr1:210001329-210001339 chr1:210001327-210001342 chr1:210001330-210001337 chr1:210001328-210001339 chr1:210001328-210001338
5	JUND	chr1:210000220-210001736	K562	blood:	n/a	chr1:210001593-210001607
6	MXI1	chr1:210000014-210002085	SK-N-SH	brain:	n/a	n/a
7	ZNF384	chr1:210000355-210001964	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209999396..210002885-chr1:210546190..210548808,3	K562	blood:
2	chr1:209995353..209998573-chr1:209998823..210001196,6	K562	blood:
3	chr1:209977871..209984485-chr1:209998424..210002427,6	K562	blood:
4	chr1:209956517..209958141-chr1:209999783..210001469,2	MCF-7	breast:
5	chr1:209991325..209994197-chr1:209997349..210000501,3	K562	blood:
6	chr1:209977871..209981214-chr1:209999703..210002866,6	K562	blood:
7	chr1:209999584..210001298-chr1:210028865..210031163,2	K562	blood:
8	chr1:209991113..209993100-chr1:209999001..210001316,2	K562	blood:
9	chr1:209977911..209983292-chr1:209996386..210001078,7	MCF-7	breast:
10	chr1:209839849..209842808-chr1:209998305..210001255,2	K562	blood:

Variant related genes	Relation type
DIEXF	TF binding region
ENSG00000162757	Chromatin interaction
ENSG00000117595	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10127937	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10218448	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489344	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119354	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582607	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11584081	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590807	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11810091	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401430	0.86[ASN][1000 genomes]
rs12403006	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12404886	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17317580	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17389541	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013196	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34743335	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753513	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766615	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41274838	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071308	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56268268	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61820635	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699507	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7526313	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544804	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546104	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932334	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs28601717	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209992600-210000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:209996000-210000800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:209996600-210000400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:209996600-210000800	Weak transcription	Liver	Liver
5	chr1:209996600-210000800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:209996600-210000800	Enhancers	HMEC	breast
7	chr1:209996800-210000600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:209996800-210000800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:209996800-210000800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:209997000-210000600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:209997000-210000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:209997000-210000800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:209997000-210000800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:209997000-210000800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:209997000-210000800	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:209997000-210000800	Weak transcription	Fetal Heart	heart
17	chr1:209997200-210000800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:209997200-210000800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:209997200-210000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:209997200-210000800	Weak transcription	Hela-S3	cervix
21	chr1:209997200-210000800	Weak transcription	HSMM	muscle
22	chr1:209997200-210001000	Weak transcription	Gastric	stomach
23	chr1:209997400-210000600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:209997400-210000800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:209997400-210000800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:209997400-210000800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:209997400-210000800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:209997400-210000800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:209997400-210000800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:209997400-210000800	Weak transcription	Adipose Nuclei	Adipose
31	chr1:209997400-210000800	Weak transcription	Left Ventricle	heart
32	chr1:209997400-210000800	Weak transcription	NH-A	brain
33	chr1:209997400-210000800	Weak transcription	NHDF-Ad	bronchial
34	chr1:209997600-210000800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:209997600-210000800	Weak transcription	Osteobl	bone
36	chr1:209998200-210000600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:209998400-210000800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:209998600-210000600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:209998600-210000600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:209998800-210000800	Enhancers	Fetal Intestine Large	intestine
41	chr1:209998800-210000800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:209999000-210000800	Enhancers	Fetal Intestine Small	intestine
43	chr1:209999200-210000600	Enhancers	HepG2	liver
44	chr1:209999400-210000400	Enhancers	A549	lung
45	chr1:209999400-210000800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:209999600-210000800	Weak transcription	HUVEC	blood vessel
47	chr1:209999800-210000400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr1:209999800-210000800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:209999800-210000800	Enhancers	NHEK	skin
50	chr1:210000000-210000800	Weak transcription	HSMMtube	muscle

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