Variant report

Variant	rs73500199
Chromosome Location	chr13:52732891-52732892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr13:52732775-52733821	GM12878	blood:	n/a	n/a
2	TBP	chr13:52732867-52733233	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr13:52732885-52734068	GM12878	blood:	n/a	n/a
4	POLR2A	chr13:52732859-52734076	SK-N-SH	brain:	n/a	n/a
5	MYC	chr13:52732634-52734062	NB4	blood:	n/a	n/a
6	POLR2A	chr13:52732745-52733981	NB4	blood:	n/a	n/a
7	SPI1	chr13:52732716-52733857	GM12878	blood:	n/a	n/a
8	YY1	chr13:52732789-52733143	SK-N-SH_RA	brain:	n/a	n/a
9	YY1	chr13:52732835-52733089	HepG2	liver:	n/a	n/a
10	MAZ	chr13:52732866-52733963	GM12878	blood:	n/a	n/a
11	YY1	chr13:52732805-52733312	SK-N-SH_RA	brain:	n/a	n/a
12	POLR2A	chr13:52732549-52734480	HepG2	liver:	n/a	n/a
13	MAX	chr13:52732867-52734101	GM12878	blood:	n/a	n/a
14	PML	chr13:52732858-52733750	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52725842..52728742-chr13:52731896..52733455,2	MCF-7	breast:
2	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: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs60691453	1.00[AMR][1000 genomes]
rs7319489	1.00[AMR][1000 genomes]
rs73500148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73500159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73500175	1.00[AMR][1000 genomes]
rs73500179	1.00[AMR][1000 genomes]
rs73500184	1.00[AMR][1000 genomes]
rs73500190	1.00[AMR][1000 genomes]
rs73500200	1.00[AMR][1000 genomes]
rs73502322	1.00[AMR][1000 genomes]
rs7999934	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52703600-52733000	Weak transcription	Esophagus	oesophagus
2	chr13:52703800-52733200	Weak transcription	Gastric	stomach
3	chr13:52704000-52733000	Weak transcription	Fetal Thymus	thymus
4	chr13:52712200-52733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:52712400-52733000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:52731600-52733000	Weak transcription	Small Intestine	intestine
7	chr13:52731800-52733000	Weak transcription	Lung	lung
8	chr13:52732000-52733000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr13:52732400-52733000	Flanking Active TSS	Brain Hippocampus Middle	brain
10	chr13:52732400-52733000	Flanking Active TSS	HepG2	liver
11	chr13:52732400-52733200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:52732400-52733200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr13:52732400-52733800	Active TSS	Stomach Mucosa	stomach
14	chr13:52732400-52734000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr13:52732600-52733000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
16	chr13:52732600-52733000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr13:52732600-52733000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr13:52732600-52733000	Enhancers	Primary T cells from cord blood	blood
19	chr13:52732600-52733000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr13:52732600-52733000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr13:52732600-52733000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr13:52732600-52733000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr13:52732600-52733000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:52732600-52733000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr13:52732600-52733000	Flanking Active TSS	Liver	Liver
26	chr13:52732600-52733000	Flanking Active TSS	Brain Angular Gyrus	brain
27	chr13:52732600-52733000	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr13:52732600-52733000	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr13:52732600-52733000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr13:52732600-52733000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:52732600-52733000	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr13:52732600-52733000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr13:52732600-52733000	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr13:52732600-52733000	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr13:52732600-52733000	Flanking Active TSS	Fetal Lung	lung
36	chr13:52732600-52733000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr13:52732600-52733000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr13:52732600-52733000	Flanking Active TSS	HMEC	breast
39	chr13:52732600-52733000	Flanking Active TSS	HSMMtube	muscle
40	chr13:52732600-52733000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr13:52732600-52733000	Flanking Active TSS	NHDF-Ad	bronchial
42	chr13:52732600-52733000	Flanking Active TSS	Osteobl	bone
43	chr13:52732600-52733200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr13:52732600-52733200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr13:52732600-52733200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr13:52732600-52733200	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr13:52732600-52733400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr13:52732600-52733600	Active TSS	Colonic Mucosa	Colon
49	chr13:52732600-52733800	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr13:52732600-52733800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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