Variant report

Variant	rs74087072
Chromosome Location	chr13:52733829-52733830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:213)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:213 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:52733337-52733829	GM12878	blood:	n/a	n/a
2	FOXA1	chr13:52733535-52734092	HepG2	liver:	n/a	n/a
3	POLR2A	chr13:52733403-52734160	HL-60	blood:	n/a	n/a
4	USF2	chr13:52733454-52734008	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr13:52733674-52734120	Hela-S3	cervix:	n/a	n/a
6	MYBL2	chr13:52733340-52734238	HepG2	liver:	n/a	n/a
7	ZBTB7A	chr13:52733213-52733877	K562	blood:	n/a	n/a
8	UBTF	chr13:52733102-52733962	K562	blood:	n/a	n/a
9	MYC	chr13:52733407-52733941	MCF-7	breast:	n/a	n/a
10	POLR2A	chr13:52733286-52734086	HUVEC	blood vessel:	n/a	n/a
11	RCOR1	chr13:52733684-52734039	Hela-S3	cervix:	n/a	n/a
12	MAX	chr13:52733593-52734110	MCF-7	breast:	n/a	n/a
13	MAX	chr13:52733105-52734312	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr13:52733329-52733926	HUVEC	blood vessel:	n/a	n/a
15	MYC	chr13:52733488-52734125	MCF10A-Er-Src	breast:	n/a	n/a
16	ELF1	chr13:52733364-52734158	HepG2	liver:	n/a	n/a
17	MYC	chr13:52733585-52734090	A549	lung:	n/a	n/a
18	E2F4	chr13:52733607-52734191	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr13:52733743-52733943	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr13:52733303-52733863	GM12892	blood:	n/a	n/a
21	POLR2A	chr13:52733493-52733973	HCT-116	colon:	n/a	n/a
22	YY1	chr13:52733602-52733916	HCT-116	colon:	n/a	n/a
23	POLR2A	chr13:52732984-52734139	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr13:52733533-52733900	H1-hESC	embryonic stem cell:	n/a	n/a
25	NFIC	chr13:52733652-52734187	HepG2	liver:	n/a	n/a
26	POLR2A	chr13:52733133-52733914	MCF-7	breast:	n/a	n/a
27	TAF1	chr13:52732922-52733927	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr13:52733313-52733898	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr13:52733254-52733856	GM15510	blood:	n/a	n/a
30	POLR2A	chr13:52733469-52734044	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAZ	chr13:52733350-52733939	K562	blood:	n/a	n/a
32	CBX3	chr13:52733555-52734397	HCT-116	colon:	n/a	n/a
33	MXI1	chr13:52732885-52734068	GM12878	blood:	n/a	n/a
34	PML	chr13:52733493-52733876	K562	blood:	n/a	n/a
35	POLR2A	chr13:52733483-52733898	K562	blood:	n/a	n/a
36	MYC	chr13:52733739-52733862	HUVEC	blood vessel:	n/a	n/a
37	MYC	chr13:52733627-52734003	H1-hESC	embryonic stem cell:	n/a	n/a
38	MBD4	chr13:52733689-52734292	HepG2	liver:	n/a	n/a
39	MAX	chr13:52733493-52734095	HepG2	liver:	n/a	n/a
40	MAX	chr13:52733650-52734237	H1-hESC	embryonic stem cell:	n/a	n/a
41	TCF12	chr13:52733685-52734009	A549	lung:	n/a	n/a
42	POLR2A	chr13:52733347-52733880	A549	lung:	n/a	n/a
43	POLR2A	chr13:52733354-52733906	A549	lung:	n/a	n/a
44	GTF2F1	chr13:52733735-52734163	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr13:52733354-52733854	HUVEC	blood vessel:	n/a	n/a
46	GABPA	chr13:52733263-52733924	K562	blood:	n/a	n/a
47	POLR2A	chr13:52733386-52733964	H1-neurons	neurons:	n/a	n/a
48	EP300	chr13:52733560-52734203	HepG2	liver:	n/a	chr13:52733650-52733666
49	EP300	chr13:52733650-52734234	HepG2	liver:	n/a	chr13:52733650-52733666
50	MXI1	chr13:52733614-52734087	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52729535..52732308-chr13:52732328..52734703,4	K562	blood:

No data

Variant related genes	Relation type
NEK3	TF binding region
ENSG00000136098	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs55896522	1.00[AMR][1000 genomes]
rs56263093	1.00[AMR][1000 genomes]
rs74087056	1.00[AMR][1000 genomes]
rs74087066	1.00[AMR][1000 genomes]
rs74087069	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74087090	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52732400-52734000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr13:52732600-52734000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:52732600-52734000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr13:52732600-52734000	Active TSS	A549	lung
5	chr13:52732600-52734000	Active TSS	NHLF	lung
6	chr13:52732600-52734200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:52732600-52734200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:52732600-52734200	Active TSS	Aorta	Aorta
9	chr13:52732800-52734000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr13:52732800-52734000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:52732800-52734000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr13:52732800-52734000	Active TSS	Left Ventricle	heart
13	chr13:52732800-52734000	Active TSS	Right Atrium	heart
14	chr13:52732800-52734000	Active TSS	Right Ventricle	heart
15	chr13:52732800-52734200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr13:52732800-52734200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:52732800-52734200	Active TSS	Fetal Brain Male	brain
18	chr13:52732800-52734200	Active TSS	Fetal Muscle Trunk	muscle
19	chr13:52732800-52734200	Active TSS	Ovary	ovary
20	chr13:52732800-52734200	Active TSS	Pancreas	Pancrea
21	chr13:52732800-52734200	Active TSS	Psoas Muscle	Psoas
22	chr13:52733000-52734000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr13:52733000-52734000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr13:52733000-52734000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr13:52733000-52734000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr13:52733000-52734000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr13:52733000-52734000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:52733000-52734000	Active TSS	Colon Smooth Muscle	Colon
29	chr13:52733000-52734000	Active TSS	Placenta Amnion	Placenta Amnion
30	chr13:52733000-52734000	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr13:52733000-52734000	Active TSS	Small Intestine	intestine
32	chr13:52733000-52734000	Flanking Bivalent TSS/Enh	Dnd41	blood
33	chr13:52733000-52734000	Active TSS	HSMM	muscle
34	chr13:52733000-52734200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr13:52733000-52734200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr13:52733000-52734200	Active TSS	HSMMtube	muscle
37	chr13:52733000-52734400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr13:52733200-52734000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr13:52733200-52734000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
40	chr13:52733200-52734000	Active TSS	Gastric	stomach
41	chr13:52733200-52734000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr13:52733200-52734200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr13:52733400-52734200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr13:52733600-52734000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr13:52733600-52734000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:52733600-52734000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
47	chr13:52733600-52734200	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr13:52733600-52734200	Active TSS	Brain Germinal Matrix	brain
49	chr13:52733600-52734200	Active TSS	Fetal Brain Female	brain
50	chr13:52733800-52734000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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