Variant report

Variant	rs11545440
Chromosome Location	chr13:53024672-53024673
allele	A/C
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	TCF12	chr13:53024513-53025099	A549	lung:	n/a	n/a
2	POLR2A	chr13:53023967-53025035	Hela-S3	cervix:	n/a	n/a
3	ZBTB7A	chr13:53024521-53025044	ECC-1	luminal epithelium:	n/a	chr13:53024910-53024919 chr13:53024789-53024798
4	GABPA	chr13:53024664-53024944	A549	lung:	n/a	chr13:53024863-53024872
5	POLR2A	chr13:53023981-53025043	HCT-116	colon:	n/a	n/a
6	E2F4	chr13:53024114-53025092	K562	blood:	n/a	chr13:53024863-53024872
7	CTCF	chr13:53024669-53025064	GM10248	blood:	n/a	chr13:53024912-53024922 chr13:53024909-53024927 chr13:53024911-53024924 chr13:53024904-53024925 chr13:53024911-53024924 chr13:53024788-53024806 chr13:53024915-53024924 chr13:53024910-53024926 chr13:53024789-53024805 chr13:53024783-53024804
8	RFX5	chr13:53024598-53025135	GM12878	blood:	n/a	n/a
9	RELA	chr13:53024002-53025103	GM19099	blood:	n/a	n/a
10	CTCF	chr13:53024555-53025027	K562	blood:	n/a	chr13:53024912-53024922 chr13:53024909-53024927 chr13:53024911-53024924 chr13:53024904-53024925 chr13:53024911-53024924 chr13:53024788-53024806 chr13:53024582-53024591 chr13:53024915-53024924 chr13:53024910-53024926 chr13:53024789-53024805 chr13:53024783-53024804
11	USF1	chr13:53024645-53024962	A549	lung:	n/a	n/a
12	MAX	chr13:53023978-53025098	K562	blood:	n/a	chr13:53024447-53024456 chr13:53024443-53024458 chr13:53024447-53024457 chr13:53024446-53024457 chr13:53024448-53024455 chr13:53024446-53024457 chr13:53024447-53024456 chr13:53024440-53024449 chr13:53024446-53024456
13	REST	chr13:53024594-53024862	PANC-1	pancreas:	n/a	n/a
14	ARID3A	chr13:53024613-53025199	HepG2	liver:	n/a	n/a
15	POLR2A	chr13:53024009-53024978	Hela-S3	cervix:	n/a	n/a
16	ATF2	chr13:53024535-53024981	H1-hESC	embryonic stem cell:	n/a	n/a
17	TAF1	chr13:53024534-53025071	H1-neurons	neurons:	n/a	n/a
18	TCF12	chr13:53024614-53025031	GM12878	blood:	n/a	n/a
19	EP300	chr13:53024520-53024953	T-47D	breast:	n/a	chr13:53024856-53024872 chr13:53024788-53024797 chr13:53024863-53024872
20	POLR2A	chr13:53024056-53024904	H1-hESC	embryonic stem cell:	n/a	n/a
21	E2F4	chr13:53023722-53025164	MCF10A-Er-Src	breast:	n/a	chr13:53024863-53024872
22	POLR2A	chr13:53024168-53024907	HepG2	liver:	n/a	n/a
23	POU2F2	chr13:53024598-53025024	GM12878	blood:	n/a	n/a
24	HDAC2	chr13:53024649-53024945	K562	blood:	n/a	n/a
25	SRF	chr13:53024564-53025153	ECC-1	luminal epithelium:	n/a	n/a
26	MXI1	chr13:53023378-53025154	IMR90	lung:	n/a	n/a
27	POLR2A	chr13:53024036-53025072	GM18951	blood:	n/a	n/a
28	SRF	chr13:53024596-53025064	ECC-1	luminal epithelium:	n/a	n/a
29	STAT5A	chr13:53024572-53024915	GM12878	blood:	n/a	n/a
30	POLR2A	chr13:53023953-53025066	GM18505	blood:	n/a	n/a
31	POLR2A	chr13:53024034-53025030	H1-hESC	embryonic stem cell:	n/a	n/a
32	REST	chr13:53023977-53025029	HL-60	blood:	n/a	n/a
33	PML	chr13:53024552-53024949	K562	blood:	n/a	n/a
34	POLR2A	chr13:53024088-53025015	K562	blood:	n/a	n/a
35	MAX	chr13:53024031-53025106	Hela-S3	cervix:	n/a	chr13:53024447-53024456 chr13:53024443-53024458 chr13:53024447-53024457 chr13:53024446-53024457 chr13:53024448-53024455 chr13:53024446-53024457 chr13:53024447-53024456 chr13:53024440-53024449 chr13:53024446-53024456
36	CREB1	chr13:53023963-53025163	GM12878	blood:	n/a	n/a
37	POLR2A	chr13:53023970-53025078	GM12892	blood:	n/a	n/a
38	MYC	chr13:53023716-53025258	MCF10A-Er-Src	breast:	n/a	chr13:53024447-53024456 chr13:53024443-53024458 chr13:53024447-53024457 chr13:53024446-53024457 chr13:53024448-53024455 chr13:53024446-53024457 chr13:53024447-53024456 chr13:53024440-53024449 chr13:53024446-53024456
39	RAD21	chr13:53024606-53025194	MCF-7	breast:	n/a	chr13:53024907-53024926 chr13:53024786-53024805 chr13:53024911-53024921
40	POLR2A	chr13:53024550-53025005	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr13:53023976-53025143	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr13:53023470-53025282	HUVEC	blood vessel:	n/a	n/a
43	NFIC	chr13:53023823-53025183	SK-N-SH	brain:	n/a	chr13:53024392-53024409 chr13:53024393-53024409
44	POLR2A	chr13:53024551-53024887	HepG2	liver:	n/a	n/a
45	CTCF	chr13:53024615-53025071	MCF-7	breast:	n/a	chr13:53024912-53024922 chr13:53024909-53024927 chr13:53024911-53024924 chr13:53024904-53024925 chr13:53024911-53024924 chr13:53024788-53024806 chr13:53024915-53024924 chr13:53024910-53024926 chr13:53024789-53024805 chr13:53024783-53024804
46	PAX5	chr13:53024561-53025007	GM12878	blood:	n/a	n/a
47	UBTF	chr13:53023995-53025004	K562	blood:	n/a	n/a
48	MAX	chr13:53024002-53025070	H1-hESC	embryonic stem cell:	n/a	chr13:53024447-53024456 chr13:53024443-53024458 chr13:53024447-53024457 chr13:53024446-53024457 chr13:53024448-53024455 chr13:53024446-53024457 chr13:53024447-53024456 chr13:53024440-53024449 chr13:53024446-53024456
49	CTCF	chr13:53024629-53025075	A549	lung:	n/a	chr13:53024912-53024922 chr13:53024909-53024927 chr13:53024911-53024924 chr13:53024904-53024925 chr13:53024911-53024924 chr13:53024788-53024806 chr13:53024915-53024924 chr13:53024910-53024926 chr13:53024789-53024805 chr13:53024783-53024804
50	CEBPD	chr13:53024545-53024944	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:201979261..201979842-chr13:53024291..53024954,2	Hela-S3	cervix:
2	chr13:53023259..53027625-chr13:53027753..53030727,5	MCF-7	breast:
3	chr13:52973921..52974578-chr13:53024315..53025276,3	MCF-7	breast:
4	chr13:53023588..53025754-chr13:53225469..53228375,2	K562	blood:
5	chr13:53023126..53025517-chr17:56734157..56736833,2	MCF-7	breast:
6	chr13:53024565..53025183-chr2:239148354..239149000,2	HCT-116	colon:

Variant related genes	Relation type
VPS36	TF binding region
CKAP2	TF binding region
ENSG00000144485	Chromatin interaction
ENSG00000234678	Chromatin interaction
ENSG00000199605	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000163435	Chromatin interaction
ENSG00000165416	Chromatin interaction
ENSG00000136108	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7335867	1.00[CHD][hapmap];1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3434605	chr13:52999509-53034851	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a
8	nsv900085	chr13:53022518-53216622	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53022600-53025000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:53022800-53024800	Active TSS	Esophagus	oesophagus
3	chr13:53022800-53025000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:53022800-53025000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr13:53022800-53025000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr13:53022800-53025200	Active TSS	NHDF-Ad	bronchial
7	chr13:53023000-53024800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:53023000-53025000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr13:53023000-53025000	Active TSS	Rectal Smooth Muscle	rectum
10	chr13:53023000-53025000	Active TSS	HSMMtube	muscle
11	chr13:53023000-53025000	Active TSS	NHLF	lung
12	chr13:53023200-53024800	Active TSS	Stomach Smooth Muscle	stomach
13	chr13:53023200-53025000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:53023200-53025000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:53023200-53025000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:53023200-53025000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:53023200-53025000	Active TSS	Muscle Satellite Cultured Cells	--
18	chr13:53023200-53025000	Active TSS	Brain Angular Gyrus	brain
19	chr13:53023200-53025000	Active TSS	Brain Anterior Caudate	brain
20	chr13:53023200-53025000	Active TSS	Fetal Intestine Small	intestine
21	chr13:53023200-53025000	Active TSS	GM12878-XiMat	blood
22	chr13:53023200-53025000	Active TSS	Hela-S3	cervix
23	chr13:53023200-53025000	Active TSS	HMEC	breast
24	chr13:53023200-53025000	Active TSS	HSMM	muscle
25	chr13:53023200-53025000	Active TSS	NHEK	skin
26	chr13:53023200-53025000	Active TSS	Osteobl	bone
27	chr13:53023200-53025200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr13:53023200-53025200	Active TSS	Colonic Mucosa	Colon
29	chr13:53023200-53025400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr13:53023400-53024800	Active TSS	Right Ventricle	heart
31	chr13:53023400-53025000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr13:53023400-53025000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:53023400-53025000	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr13:53023400-53025000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr13:53023400-53025000	Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr13:53023400-53025000	Active TSS	Brain Hippocampus Middle	brain
37	chr13:53023400-53025000	Active TSS	Fetal Kidney	kidney
38	chr13:53023400-53025000	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr13:53023400-53025200	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr13:53023400-53025200	Active TSS	Psoas Muscle	Psoas
41	chr13:53023400-53025200	Active TSS	A549	lung
42	chr13:53023600-53024800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr13:53023600-53024800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr13:53023600-53024800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr13:53023600-53024800	Active TSS	Fetal Muscle Trunk	muscle
46	chr13:53023600-53024800	Active TSS	Placenta	Placenta
47	chr13:53023600-53024800	Active TSS	Left Ventricle	heart
48	chr13:53023600-53024800	Active TSS	Lung	lung
49	chr13:53023600-53024800	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr13:53023600-53025000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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