Variant report

Variant	rs9563094
Chromosome Location	chr13:52734011-52734012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:118)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:118 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr13:52733535-52734092	HepG2	liver:	n/a	n/a
2	POLR2A	chr13:52733403-52734160	HL-60	blood:	n/a	n/a
3	CEBPB	chr13:52733674-52734120	Hela-S3	cervix:	n/a	n/a
4	MYBL2	chr13:52733340-52734238	HepG2	liver:	n/a	n/a
5	POLR2A	chr13:52733286-52734086	HUVEC	blood vessel:	n/a	n/a
6	RCOR1	chr13:52733684-52734039	Hela-S3	cervix:	n/a	n/a
7	MAX	chr13:52733593-52734110	MCF-7	breast:	n/a	n/a
8	MAX	chr13:52733105-52734312	ECC-1	luminal epithelium:	n/a	n/a
9	MYC	chr13:52733488-52734125	MCF10A-Er-Src	breast:	n/a	n/a
10	ELF1	chr13:52733364-52734158	HepG2	liver:	n/a	n/a
11	MYC	chr13:52733585-52734090	A549	lung:	n/a	n/a
12	E2F4	chr13:52733607-52734191	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr13:52732984-52734139	MCF10A-Er-Src	breast:	n/a	n/a
14	NFIC	chr13:52733652-52734187	HepG2	liver:	n/a	n/a
15	POLR2A	chr13:52733469-52734044	H1-hESC	embryonic stem cell:	n/a	n/a
16	CBX3	chr13:52733555-52734397	HCT-116	colon:	n/a	n/a
17	MXI1	chr13:52732885-52734068	GM12878	blood:	n/a	n/a
18	MBD4	chr13:52733689-52734292	HepG2	liver:	n/a	n/a
19	MAX	chr13:52733493-52734095	HepG2	liver:	n/a	n/a
20	MAX	chr13:52733650-52734237	H1-hESC	embryonic stem cell:	n/a	n/a
21	GTF2F1	chr13:52733735-52734163	Hela-S3	cervix:	n/a	n/a
22	MAFK	chr13:52733863-52734073	Hela-S3	cervix:	n/a	n/a
23	EP300	chr13:52733560-52734203	HepG2	liver:	n/a	chr13:52733650-52733666
24	EP300	chr13:52733650-52734234	HepG2	liver:	n/a	chr13:52733650-52733666
25	MXI1	chr13:52733614-52734087	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr13:52733405-52734096	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr13:52732971-52734089	Hela-S3	cervix:	n/a	n/a
28	E2F6	chr13:52733246-52734133	K562	blood:	n/a	n/a
29	BHLHE40	chr13:52733132-52734017	K562	blood:	n/a	n/a
30	POLR2A	chr13:52733011-52734033	Hela-S3	cervix:	n/a	n/a
31	MAX	chr13:52733614-52734094	HUVEC	blood vessel:	n/a	n/a
32	E2F6	chr13:52733091-52734548	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr13:52732859-52734076	SK-N-SH	brain:	n/a	n/a
34	MYC	chr13:52733677-52734082	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr13:52732970-52734237	MCF10A-Er-Src	breast:	n/a	n/a
36	EP300	chr13:52733773-52734152	GM12878	blood:	n/a	n/a
37	TCF7L2	chr13:52733086-52734068	Hela-S3	cervix:	n/a	n/a
38	MYC	chr13:52732634-52734062	NB4	blood:	n/a	n/a
39	KAP1	chr13:52733319-52734204	HEK293	kidney:	n/a	n/a
40	SIN3A	chr13:52732989-52734210	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr13:52733542-52734013	K562	blood:	n/a	n/a
42	MAX	chr13:52733634-52734055	Hela-S3	cervix:	n/a	n/a
43	TCF12	chr13:52733451-52734234	A549	lung:	n/a	n/a
44	CEBPB	chr13:52733770-52734105	A549	lung:	n/a	n/a
45	TBP	chr13:52733504-52734239	HepG2	liver:	n/a	n/a
46	POLR2A	chr13:52732918-52734186	SK-N-MC	brain:	n/a	n/a
47	MXI1	chr13:52733340-52734161	HepG2	liver:	n/a	n/a
48	HA-E2F1	chr13:52733104-52734181	MCF-7	breast:	n/a	n/a
49	E2F6	chr13:52733039-52734363	K562	blood:	n/a	n/a
50	CBX3	chr13:52733509-52734229	HCT-116	colon:	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: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17069418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4520725	1.00[AFR][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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52732600-52734200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:52732600-52734200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:52732600-52734200	Active TSS	Aorta	Aorta
4	chr13:52732800-52734200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:52732800-52734200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:52732800-52734200	Active TSS	Fetal Brain Male	brain
7	chr13:52732800-52734200	Active TSS	Fetal Muscle Trunk	muscle
8	chr13:52732800-52734200	Active TSS	Ovary	ovary
9	chr13:52732800-52734200	Active TSS	Pancreas	Pancrea
10	chr13:52732800-52734200	Active TSS	Psoas Muscle	Psoas
11	chr13:52733000-52734200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr13:52733000-52734200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr13:52733000-52734200	Active TSS	HSMMtube	muscle
14	chr13:52733000-52734400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr13:52733200-52734200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:52733400-52734200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr13:52733600-52734200	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr13:52733600-52734200	Active TSS	Brain Germinal Matrix	brain
19	chr13:52733600-52734200	Active TSS	Fetal Brain Female	brain
20	chr13:52733800-52734200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr13:52733800-52734200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:52733800-52734200	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr13:52733800-52734200	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr13:52733800-52734200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr13:52733800-52734200	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr13:52733800-52734200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr13:52733800-52734200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr13:52733800-52734200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr13:52733800-52734200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr13:52733800-52734200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr13:52733800-52734200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr13:52733800-52734200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr13:52733800-52734200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr13:52733800-52734200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr13:52733800-52734200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr13:52733800-52734200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr13:52733800-52734200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr13:52733800-52734200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr13:52733800-52734200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:52733800-52734200	Flanking Active TSS	Liver	Liver
41	chr13:52733800-52734200	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr13:52733800-52734200	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr13:52733800-52734200	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr13:52733800-52734200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr13:52733800-52734200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:52733800-52734200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr13:52733800-52734200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr13:52733800-52734200	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr13:52733800-52734200	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr13:52733800-52734200	Flanking Active TSS	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links