Variant report

Variant	rs13133792
Chromosome Location	chr4:57845269-57845270
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:300)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:300 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr4:57842986-57845530	K562	blood:	n/a	n/a
2	ZBTB33	chr4:57844724-57845269	SK-N-SH	brain:	n/a	n/a
3	SIN3A	chr4:57844701-57846119	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:57844770-57845357	ECC-1	luminal epithelium:	n/a	n/a
5	TCF7L2	chr4:57844802-57845420	HCT-116	colon:	n/a	n/a
6	ELK4	chr4:57844868-57845325	Hela-S3	cervix:	n/a	n/a
7	RCOR1	chr4:57844836-57845426	HepG2	liver:	n/a	n/a
8	CHD2	chr4:57844759-57845458	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr4:57844673-57845592	K562	blood:	n/a	n/a
10	MYC	chr4:57844819-57845407	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr4:57844517-57845506	U87	brain:	n/a	n/a
12	CHD2	chr4:57844741-57845471	K562	blood:	n/a	n/a
13	POLR2A	chr4:57844722-57845613	GM12891	blood:	n/a	n/a
14	POLR2A	chr4:57844662-57845462	MCF-7	breast:	n/a	n/a
15	TAF1	chr4:57844674-57845518	ECC-1	luminal epithelium:	n/a	n/a
16	SIN3AK20	chr4:57844686-57845372	PANC-1	pancreas:	n/a	n/a
17	FOXM1	chr4:57844676-57845280	GM12878	blood:	n/a	n/a
18	SIN3A	chr4:57844769-57845433	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:57844515-57845649	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:57844690-57845413	GM18951	blood:	n/a	n/a
21	POLR2A	chr4:57843025-57845454	GM19193	blood:	n/a	n/a
22	RUNX3	chr4:57844610-57845493	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:57844695-57845350	K562	blood:	n/a	n/a
24	POLR2A	chr4:57844607-57846114	GM12878	blood:	n/a	n/a
25	ZNF384	chr4:57844766-57845425	K562	blood:	n/a	n/a
26	GABPA	chr4:57844790-57845356	SK-N-SH	brain:	n/a	n/a
27	CBX3	chr4:57844773-57845483	K562	blood:	n/a	n/a
28	POLR2A	chr4:57844657-57845357	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr4:57844703-57845510	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:57844656-57845539	K562	blood:	n/a	n/a
31	MAX	chr4:57844603-57845489	HCT-116	colon:	n/a	n/a
32	POLR2A	chr4:57843483-57845482	K562	blood:	n/a	n/a
33	MAX	chr4:57844699-57845275	MCF-7	breast:	n/a	n/a
34	SRF	chr4:57844754-57845426	MCF-7	breast:	n/a	n/a
35	SIN3AK20	chr4:57844767-57845412	HepG2	liver:	n/a	n/a
36	TBL1XR1	chr4:57844740-57845487	K562	blood:	n/a	n/a
37	GTF2F1	chr4:57844844-57845484	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr4:57844503-57845546	K562	blood:	n/a	n/a
39	POLR2A	chr4:57843031-57845484	NB4	blood:	n/a	n/a
40	POLR2A	chr4:57844712-57845419	GM12878	blood:	n/a	n/a
41	CEBPB	chr4:57844900-57845351	IMR90	lung:	n/a	n/a
42	POLR2A	chr4:57844660-57845380	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr4:57844705-57845478	PBDE	blood:	n/a	n/a
44	POLR2A	chr4:57844698-57845477	K562	blood:	n/a	n/a
45	MAX	chr4:57844696-57845551	ECC-1	luminal epithelium:	n/a	n/a
46	MYC	chr4:57844367-57845543	K562	blood:	n/a	n/a
47	E2F6	chr4:57845165-57845351	K562	blood:	n/a	chr4:57845263-57845273
48	TEAD4	chr4:57844668-57845540	K562	blood:	n/a	n/a
49	EP300	chr4:57844707-57845316	K562	blood:	n/a	n/a
50	POLR2A	chr4:57844705-57845327	HEK293	kidney:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57301138..57303431-chr4:57844871..57846919,2	MCF-7	breast:
2	chr4:57844609..57846562-chr4:57874022..57876813,2	K562	blood:
3	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:
4	chr4:57822641..57828782-chr4:57838494..57846737,10	K562	blood:
5	chr20:52556025..52558052-chr4:57843937..57845567,2	MCF-7	breast:
6	chr4:57843255..57845274-chr4:57888366..57890332,2	K562	blood:
7	chr4:57332287..57335313-chr4:57842375..57846822,5	K562	blood:
8	chr12:120729556..120730230-chr4:57844498..57845451,2	Hela-S3	cervix:
9	chr4:57845155..57847188-chr4:57856587..57858696,2	MCF-7	breast:
10	chr4:57772839..57777394-chr4:57841397..57848240,17	K562	blood:
11	chr4:57773933..57775544-chr4:57843880..57845543,2	MCF-7	breast:
12	chr4:57332264..57334926-chr4:57844078..57846239,2	MCF-7	breast:
13	chr4:57771688..57776264-chr4:57841866..57845328,7	MCF-7	breast:

No data

Variant related genes	Relation type
NOA1	TF binding region
ENSG00000128059	Chromatin interaction
ENSG00000269949	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000236352	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10002269	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10018580	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10018619	0.85[EUR][1000 genomes]
rs10033214	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10034163	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1107675	0.84[CEU][hapmap]
rs11573115	0.83[CEU][hapmap]
rs11930475	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs11932673	0.88[TSI][hapmap]
rs11936394	0.94[AFR][1000 genomes]
rs11940411	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11947717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13125046	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13145285	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1568260	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17087291	0.83[AFR][1000 genomes]
rs17087332	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17087382	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17181222	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs34278765	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34601747	1.00[AFR][1000 genomes]
rs34749389	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35437996	0.89[AFR][1000 genomes]
rs35706166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71601666	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71601672	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7440152	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7659855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7684271	0.92[EUR][1000 genomes]
rs9991234	0.84[AMR][1000 genomes];1.00[EUR][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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13133792	IFNGR1	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57840800-57846800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:57841400-57846200	Active TSS	HMEC	breast
3	chr4:57841400-57846200	Active TSS	NHEK	skin
4	chr4:57841400-57846400	Active TSS	GM12878-XiMat	blood
5	chr4:57841400-57846600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:57841400-57846600	Active TSS	Hela-S3	cervix
7	chr4:57841600-57846600	Active TSS	NHLF	lung
8	chr4:57841800-57846400	Active TSS	Fetal Intestine Large	intestine
9	chr4:57842000-57846000	Active TSS	Gastric	stomach
10	chr4:57842000-57846200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:57842000-57846200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr4:57842000-57846200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:57842000-57846200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr4:57842000-57846200	Active TSS	Fetal Kidney	kidney
15	chr4:57842000-57846200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr4:57842000-57846200	Active TSS	Ovary	ovary
17	chr4:57842000-57846400	Active TSS	Fetal Intestine Small	intestine
18	chr4:57842000-57846600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr4:57842000-57846600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr4:57842000-57846600	Active TSS	HSMM	muscle
21	chr4:57842000-57846600	Active TSS	K562	blood
22	chr4:57842000-57846800	Active TSS	HSMMtube	muscle
23	chr4:57842000-57847000	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr4:57842000-57847000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:57842000-57847000	Active TSS	A549	lung
26	chr4:57842200-57846000	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr4:57842200-57846000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:57842200-57846000	Active TSS	Lung	lung
29	chr4:57842200-57846000	Active TSS	Small Intestine	intestine
30	chr4:57842200-57846000	Active TSS	Stomach Mucosa	stomach
31	chr4:57842200-57846600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:57842400-57846000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:57842400-57846200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:57842600-57845800	Active TSS	Colon Smooth Muscle	Colon
35	chr4:57842600-57846000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:57842600-57846000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:57842600-57846000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr4:57842600-57846000	Active TSS	Aorta	Aorta
39	chr4:57842600-57846000	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr4:57842600-57846000	Active TSS	Spleen	Spleen
41	chr4:57842600-57846200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:57842600-57846200	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr4:57842600-57846200	Active TSS	Fetal Lung	lung
44	chr4:57842600-57846200	Active TSS	Osteobl	bone
45	chr4:57842600-57846400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:57842600-57846600	Active TSS	NHDF-Ad	bronchial
47	chr4:57842800-57845600	Active TSS	Brain Anterior Caudate	brain
48	chr4:57842800-57845600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr4:57842800-57845800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:57842800-57845800	Active TSS	Brain Angular Gyrus	brain

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