Variant report

Variant	rs747781
Chromosome Location	chr13:52553102-52553103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr13:52552903-52553484	K562	blood:	n/a	n/a
2	HEY1	chr13:52552946-52553399	K562	blood:	n/a	n/a
3	MAX	chr13:52552954-52553399	K562	blood:	n/a	n/a
4	EP300	chr13:52553045-52553532	HepG2	liver:	n/a	n/a
5	EP300	chr13:52552907-52553431	K562	blood:	n/a	n/a
6	BHLHE40	chr13:52552947-52553274	K562	blood:	n/a	n/a
7	RCOR1	chr13:52552886-52553450	K562	blood:	n/a	n/a
8	HNF4A	chr13:52553048-52553492	HepG2	liver:	n/a	chr13:52553245-52553260
9	CEBPD	chr13:52553057-52553384	HepG2	liver:	n/a	n/a
10	ATF1	chr13:52552888-52553465	K562	blood:	n/a	n/a
11	JUND	chr13:52552975-52553469	K562	blood:	n/a	n/a
12	ZNF143	chr13:52552997-52553376	K562	blood:	n/a	n/a
13	SMC3	chr13:52553077-52553438	HepG2	liver:	n/a	n/a
14	ATF3	chr13:52553100-52553433	K562	blood:	n/a	n/a
15	EP300	chr13:52553048-52553344	HepG2	liver:	n/a	n/a
16	CBX3	chr13:52552933-52553521	K562	blood:	n/a	n/a
17	CEBPD	chr13:52553054-52553409	HepG2	liver:	n/a	n/a
18	SP1	chr13:52553004-52553558	HepG2	liver:	n/a	n/a
19	MAX	chr13:52552937-52553591	HepG2	liver:	n/a	n/a
20	FOXA1	chr13:52552991-52553489	HepG2	liver:	n/a	n/a
21	USF1	chr13:52552920-52553507	K562	blood:	n/a	n/a
22	MYC	chr13:52552844-52553419	K562	blood:	n/a	n/a
23	TAF1	chr13:52552976-52553273	K562	blood:	n/a	n/a
24	NFYB	chr13:52553086-52553489	K562	blood:	n/a	n/a
25	HDAC2	chr13:52553039-52553413	HepG2	liver:	n/a	n/a
26	ARID3A	chr13:52553095-52553479	HepG2	liver:	n/a	n/a
27	USF1	chr13:52553065-52553559	HCT-116	colon:	n/a	n/a
28	CEBPB	chr13:52552875-52553551	K562	blood:	n/a	chr13:52553277-52553288
29	ZNF384	chr13:52553067-52553204	K562	blood:	n/a	n/a
30	ARID3A	chr13:52553083-52553442	K562	blood:	n/a	n/a
31	CEBPB	chr13:52553016-52553495	HepG2	liver:	n/a	chr13:52553277-52553288
32	TAL1	chr13:52552984-52553413	K562	blood:	n/a	n/a
33	CREB1	chr13:52552965-52553576	HepG2	liver:	n/a	n/a
34	MAX	chr13:52552899-52553459	K562	blood:	n/a	n/a
35	CREB1	chr13:52552941-52553602	HepG2	liver:	n/a	n/a
36	FOXA2	chr13:52553099-52553487	HepG2	liver:	n/a	n/a
37	POLR2A	chr13:52552969-52553498	K562	blood:	n/a	n/a
38	HNF4A	chr13:52552969-52553401	HepG2	liver:	n/a	chr13:52553245-52553260
39	HNF4G	chr13:52553090-52553470	HepG2	liver:	n/a	chr13:52553244-52553259
40	NFIC	chr13:52553062-52553499	HepG2	liver:	n/a	n/a
41	MYC	chr13:52552730-52553533	K562	blood:	n/a	n/a
42	CEBPB	chr13:52553064-52553389	K562	blood:	n/a	chr13:52553277-52553288
43	MAZ	chr13:52552969-52553389	HepG2	liver:	n/a	n/a
44	CEBPD	chr13:52552983-52553543	K562	blood:	n/a	n/a
45	UBTF	chr13:52553055-52553195	K562	blood:	n/a	n/a
46	CEBPB	chr13:52552982-52553509	HepG2	liver:	n/a	chr13:52553277-52553288
47	GATA1	chr13:52552498-52553635	PBDE	blood:	n/a	n/a
48	MXI1	chr13:52552999-52553476	HepG2	liver:	n/a	n/a
49	FOXA1	chr13:52553038-52553595	HepG2	liver:	n/a	n/a
50	ATF3	chr13:52553085-52553510	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52547935..52549465-chr13:52552409..52555264,2	K562	blood:
2	chr13:52549808..52551859-chr13:52553072..52555669,2	K562	blood:

No data

Variant related genes	Relation type
ATP7B	TF binding region
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1004576	0.91[CHB][hapmap]
rs1051332	0.82[GIH][hapmap]
rs1055062	0.91[CHB][hapmap]
rs1060631	0.91[CHB][hapmap]
rs11620583	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12146904	0.91[CHB][hapmap]
rs12431310	0.91[CHB][hapmap]
rs1571189	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1801243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1801244	0.96[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs1886538	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1886542	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1886543	0.91[CHB][hapmap]
rs1886544	0.91[CHB][hapmap]
rs1886547	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs1924611	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1951922	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2004866	0.89[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap]
rs2147363	0.82[CHD][hapmap]
rs2181891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274202	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2277448	0.91[CHB][hapmap]
rs2296246	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs2296347	0.91[CHB][hapmap]
rs2296348	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2296349	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2408544	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2408550	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs2408551	0.82[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs2408552	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs2408554	0.91[CHB][hapmap]
rs2408609	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2408611	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2897964	0.91[CHB][hapmap]
rs2897977	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3368	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3742288	0.96[CEU][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs3742289	0.91[CHB][hapmap]
rs3783242	0.91[CHB][hapmap]
rs3818422	0.91[CHB][hapmap]
rs3825526	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs3825527	0.96[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs3825528	0.89[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs4297592	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4497567	0.91[CHB][hapmap]
rs4941727	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs6561656	0.91[CHB][hapmap]
rs732071	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7320831	0.91[CHB][hapmap]
rs7321120	0.91[CHB][hapmap]
rs7321435	0.89[ASW][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.82[MKK][hapmap]
rs7324458	0.91[CHB][hapmap]
rs7327634	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs750290	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs752570	0.82[EUR][1000 genomes]
rs754610	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs755363	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs7981904	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs7991237	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs7994928	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7995946	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs7998770	0.91[CHB][hapmap]
rs7999812	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs9316563	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526812	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs9526814	0.85[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs9526819	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526823	0.91[CHB][hapmap]
rs9526825	0.91[CHB][hapmap]
rs9526837	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9526841	0.91[CHB][hapmap]
rs9526842	0.86[JPT][hapmap]
rs9535812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535817	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535819	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535822	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535823	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535825	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9535826	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535828	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs9535832	0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs9535836	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9535851	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9535856	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9535858	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9535861	0.82[CHB][hapmap]
rs9535862	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9535866	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9535867	0.91[CHB][hapmap]
rs9535873	0.91[CHB][hapmap]
rs9535878	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9535879	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs9535880	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9535882	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9535885	0.86[JPT][hapmap]
rs9535887	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9563089	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9568677	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs9568681	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568682	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9568684	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs9568713	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][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	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	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	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
5	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1041996	chr13:52544805-52581501	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
8	esv2763022	chr13:52544978-52581513	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs747781	CKAP2	cis	parietal	SCAN
rs747781	ALG11	cis	Artery Tibial	GTEx
rs747781	CKAP2	cis	cerebellum	SCAN
rs747781	NCRNA00282	cis	cerebellum	SCAN
rs747781	ALG11	cis	Muscle Skeletal	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
3	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr13:52530200-52555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:52534400-52555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:52540000-52554600	Weak transcription	HSMMtube	muscle
8	chr13:52541400-52554800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:52544800-52554400	Weak transcription	Brain Anterior Caudate	brain
10	chr13:52544800-52556600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr13:52545000-52555400	Weak transcription	Adipose Nuclei	Adipose
12	chr13:52545000-52555600	Weak transcription	Aorta	Aorta
13	chr13:52545400-52555400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:52549000-52555400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr13:52549000-52555600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr13:52550200-52554200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr13:52551600-52555800	Enhancers	Fetal Intestine Small	intestine
18	chr13:52551800-52554800	Enhancers	Fetal Heart	heart
19	chr13:52552600-52553600	Flanking Active TSS	K562	blood
20	chr13:52552600-52554400	Enhancers	Fetal Intestine Large	intestine
21	chr13:52552600-52555800	Enhancers	Stomach Mucosa	stomach
22	chr13:52552800-52553200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr13:52552800-52553200	Flanking Active TSS	HepG2	liver
24	chr13:52552800-52553400	Enhancers	Duodenum Mucosa	Duodenum
25	chr13:52552800-52553400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr13:52553000-52553200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr13:52553000-52553200	Enhancers	Fetal Muscle Trunk	muscle
28	chr13:52553000-52553200	Enhancers	Gastric	stomach
29	chr13:52553000-52553400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:52553000-52553400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:52553000-52553400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr13:52553000-52553400	Enhancers	Placenta	Placenta
33	chr13:52553000-52553400	Enhancers	Left Ventricle	heart
34	chr13:52553000-52553400	Enhancers	Ovary	ovary
35	chr13:52553000-52553400	Enhancers	Pancreas	Pancrea
36	chr13:52553000-52553400	Enhancers	Psoas Muscle	Psoas
37	chr13:52553000-52553400	Enhancers	Right Atrium	heart
38	chr13:52553000-52553400	Enhancers	Right Ventricle	heart
39	chr13:52553000-52553600	Flanking Active TSS	Liver	Liver
40	chr13:52553000-52555800	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links