Variant report

Variant	rs13319192
Chromosome Location	chr3:53193548-53193549
allele	G/T
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	SIN3AK20	chr3:53193446-53193840	HepG2	liver:	n/a	n/a
2	TBP	chr3:53193451-53194181	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:53193329-53193869	HepG2	liver:	n/a	n/a
4	NFIC	chr3:53193372-53194013	ECC-1	luminal epithelium:	n/a	n/a
5	RCOR1	chr3:53193201-53194060	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:53193364-53193880	HepG2	liver:	n/a	n/a
7	HNF4A	chr3:53193328-53193859	HepG2	liver:	n/a	chr3:53193694-53193707 chr3:53193693-53193707 chr3:53193693-53193706 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53193689-53193711 chr3:53193691-53193709 chr3:53193693-53193707 chr3:53193694-53193706 chr3:53193698-53193710 chr3:53193692-53193707 chr3:53193693-53193706 chr3:53193693-53193706 chr3:53193695-53193707
8	MAX	chr3:53193548-53193888	HepG2	liver:	n/a	n/a
9	FOXA1	chr3:53193445-53193973	HepG2	liver:	n/a	n/a
10	SPI1	chr3:53192518-53193578	HL-60	blood:	n/a	chr3:53192891-53192900 chr3:53192890-53192903 chr3:53192890-53192903 chr3:53192889-53192902
11	REST	chr3:53193486-53193887	HepG2	liver:	n/a	chr3:53193588-53193601
12	RXRA	chr3:53193400-53193901	HepG2	liver:	n/a	chr3:53193692-53193708 chr3:53193725-53193739 chr3:53193690-53193710 chr3:53193692-53193706 chr3:53193698-53193707 chr3:53193693-53193706 chr3:53193693-53193706
13	YY1	chr3:53193351-53193919	HepG2	liver:	n/a	n/a
14	ZNF143	chr3:53193120-53193829	H1-hESC	embryonic stem cell:	n/a	chr3:53193763-53193781 chr3:53193759-53193774
15	POLR2A	chr3:53193368-53193960	HepG2	liver:	n/a	n/a
16	SIN3A	chr3:53193448-53193814	H1-hESC	embryonic stem cell:	n/a	chr3:53193788-53193802
17	MYBL2	chr3:53193309-53194008	HepG2	liver:	n/a	n/a
18	FOXA1	chr3:53193363-53193908	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:53193400-53193902	Hela-S3	cervix:	n/a	n/a
20	RAD21	chr3:53193464-53193658	HepG2	liver:	n/a	n/a
21	HNF4G	chr3:53193396-53193929	HepG2	liver:	n/a	chr3:53193694-53193707 chr3:53193693-53193707 chr3:53193693-53193706 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53193689-53193711 chr3:53193691-53193709 chr3:53193693-53193707 chr3:53193691-53193706 chr3:53193694-53193706 chr3:53193698-53193710 chr3:53193693-53193706 chr3:53193693-53193706 chr3:53193695-53193707
22	EP300	chr3:53193435-53193939	HepG2	liver:	n/a	n/a
23	NFIC	chr3:53193341-53193943	HepG2	liver:	n/a	n/a
24	MAX	chr3:53193381-53193957	ECC-1	luminal epithelium:	n/a	n/a
25	GATA2	chr3:53193287-53193709	HUVEC	blood vessel:	n/a	n/a
26	EP300	chr3:53193442-53193928	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:53193397-53193967	HepG2	liver:	n/a	n/a
28	SMC3	chr3:53193345-53193839	HepG2	liver:	n/a	chr3:53193543-53193550
29	CTCF	chr3:53193540-53193690	HPAF	blood vessel:	n/a	n/a
30	CTCF	chr3:53193540-53193690	HepG2	liver:	n/a	n/a
31	HEY1	chr3:53193278-53194047	HepG2	liver:	n/a	n/a
32	MAZ	chr3:53193223-53193926	HepG2	liver:	n/a	n/a
33	SMC3	chr3:53193405-53193554	Hela-S3	cervix:	n/a	chr3:53193543-53193550
34	MBD4	chr3:53193235-53193928	HepG2	liver:	n/a	n/a
35	MXI1	chr3:53193378-53195621	HepG2	liver:	n/a	n/a
36	MYBL2	chr3:53193214-53193795	HepG2	liver:	n/a	n/a
37	CTCF	chr3:53193420-53193570	HepG2	liver:	n/a	n/a
38	HNF4A	chr3:53193315-53193934	HepG2	liver:	n/a	chr3:53193694-53193707 chr3:53193693-53193707 chr3:53193693-53193706 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53193689-53193711 chr3:53193691-53193709 chr3:53193693-53193707 chr3:53193694-53193706 chr3:53193698-53193710 chr3:53193692-53193707 chr3:53193693-53193706 chr3:53193693-53193706 chr3:53193695-53193707
39	REST	chr3:53193042-53193588	H1-hESC	embryonic stem cell:	n/a	n/a
40	BACH1	chr3:53193536-53193744	H1-hESC	embryonic stem cell:	n/a	n/a
41	HNF4G	chr3:53193347-53194323	HepG2	liver:	n/a	chr3:53193694-53193707 chr3:53193693-53193707 chr3:53193693-53193706 chr3:53194212-53194227 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53194212-53194227 chr3:53194210-53194228 chr3:53193689-53193711 chr3:53193691-53193709 chr3:53194213-53194225 chr3:53194213-53194225 chr3:53194212-53194227 chr3:53194218-53194226 chr3:53193693-53193707 chr3:53193691-53193706 chr3:53193694-53193706 chr3:53194212-53194226 chr3:53194210-53194225 chr3:53193698-53193710 chr3:53194212-53194227 chr3:53193693-53193706 chr3:53194212-53194226 chr3:53194213-53194226 chr3:53193693-53193706 chr3:53193695-53193707
42	ZNF263	chr3:53193372-53194115	HEK293-T-REx	kidney:	n/a	n/a
43	FOXA2	chr3:53193175-53194262	HepG2	liver:	n/a	n/a
44	NR2F2	chr3:53193374-53194035	MCF-7	breast:	n/a	chr3:53193695-53193710
45	FOXA2	chr3:53193394-53194027	A549	lung:	n/a	n/a
46	POLR2A	chr3:53193357-53193707	HUVEC	blood vessel:	n/a	n/a
47	FOS	chr3:53193175-53193676	HUVEC	blood vessel:	n/a	n/a
48	FOXA1	chr3:53193135-53194015	HepG2	liver:	n/a	n/a
49	FOXA2	chr3:53193468-53193899	HepG2	liver:	n/a	n/a
50	EP300	chr3:53193433-53193854	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
2	chr16:30758613..30761206-chr3:53192006..53193731,2	MCF-7	breast:
3	chr3:53150117..53153813-chr3:53191442..53194922,3	MCF-7	breast:
4	chr3:53167017..53169952-chr3:53191720..53194469,2	K562	blood:

Variant related genes	Relation type
PRKCD	TF binding region
ENSG00000156873	Chromatin interaction
ENSG00000163933	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2035451	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56972966	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59254509	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967449	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750527	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750528	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862206	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13319192	TKT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53182400-53193800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:53183200-53194600	Enhancers	Gastric	stomach
3	chr3:53183400-53194600	Enhancers	Pancreas	Pancrea
4	chr3:53184200-53194400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:53184400-53193800	Enhancers	Adipose Nuclei	Adipose
6	chr3:53187800-53194600	Enhancers	Esophagus	oesophagus
7	chr3:53189600-53194000	Enhancers	Stomach Mucosa	stomach
8	chr3:53190200-53194200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:53190600-53194000	Enhancers	Colonic Mucosa	Colon
10	chr3:53190600-53194400	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr3:53190800-53194600	Enhancers	Lung	lung
12	chr3:53191000-53194400	Enhancers	Fetal Intestine Small	intestine
13	chr3:53191200-53194400	Enhancers	Placenta	Placenta
14	chr3:53191400-53194400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:53191400-53194400	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:53191400-53194400	Enhancers	Fetal Intestine Large	intestine
17	chr3:53191600-53194000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:53191800-53194200	Enhancers	Brain Hippocampus Middle	brain
19	chr3:53191800-53194200	Weak transcription	HMEC	breast
20	chr3:53191800-53194400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:53191800-53194400	Enhancers	Right Ventricle	heart
22	chr3:53192000-53194600	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:53192200-53194000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:53192200-53194400	Enhancers	Primary B cells from cord blood	blood
25	chr3:53192400-53193600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr3:53192400-53194000	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr3:53192400-53194600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:53192400-53194600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:53192400-53194600	Enhancers	Liver	Liver
30	chr3:53192600-53194200	Enhancers	GM12878-XiMat	blood
31	chr3:53192600-53194400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:53192600-53194600	Enhancers	Fetal Kidney	kidney
33	chr3:53192600-53194600	Flanking Active TSS	HepG2	liver
34	chr3:53192600-53194800	Enhancers	Spleen	Spleen
35	chr3:53192800-53193600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr3:53192800-53193800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:53192800-53193800	Weak transcription	Brain Anterior Caudate	brain
38	chr3:53192800-53194200	Weak transcription	Brain Angular Gyrus	brain
39	chr3:53192800-53194400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
40	chr3:53192800-53194400	Enhancers	Right Atrium	heart
41	chr3:53192800-53194400	Enhancers	HUVEC	blood vessel
42	chr3:53192800-53194600	Enhancers	Fetal Lung	lung
43	chr3:53193000-53193800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:53193000-53194000	Weak transcription	Small Intestine	intestine
45	chr3:53193000-53194200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
46	chr3:53193000-53194400	Weak transcription	Aorta	Aorta
47	chr3:53193200-53193600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:53193200-53193600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:53193200-53193600	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr3:53193200-53193600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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