Variant report

Variant	rs1010552
Chromosome Location	chr3:52540544-52540545
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	MAX	chr3:52540376-52540617	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr3:52540206-52540768	HEK293-T-REx	kidney:	n/a	chr3:52540447-52540468
3	MAX	chr3:52540250-52540719	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52539372..52542636-chr3:52569567..52572921,4	MCF-7	breast:
2	chr3:52539497..52541037-chr3:52553814..52556240,2	MCF-7	breast:
3	chr3:52539792..52541522-chr3:52570415..52572331,2	K562	blood:

Variant related genes	Relation type
STAB1	TF binding region
ENSG00000168273	Chromatin interaction
ENSG00000010327	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1010553	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs1010554	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs10510760	0.84[CHB][hapmap]
rs10865973	0.85[CHB][hapmap]
rs10865974	0.84[CHB][hapmap]
rs1108842	0.84[CHB][hapmap]
rs11130306	0.93[ASN][1000 genomes]
rs11130310	0.84[CHB][hapmap]
rs11130312	0.85[CHB][hapmap]
rs11130315	0.84[CHB][hapmap]
rs11130317	0.84[CHB][hapmap]
rs11177	0.84[CHB][hapmap]
rs1133415	0.84[CHB][hapmap]
rs11714419	0.84[CHB][hapmap]
rs11714565	0.84[CHB][hapmap]
rs11720159	0.85[CHB][hapmap]
rs11720243	0.84[CHB][hapmap]
rs12487445	0.84[CHB][hapmap]
rs12487591	0.84[CHB][hapmap]
rs12489732	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12489828	0.89[CHB][hapmap]
rs12496634	0.84[CHB][hapmap]
rs12635140	0.84[CHB][hapmap]
rs13063160	0.89[CHB][hapmap]
rs13064064	0.84[CHB][hapmap]
rs13068293	0.84[CHB][hapmap]
rs13081028	0.90[CHB][hapmap]
rs13083798	0.84[CHB][hapmap]
rs13085895	0.85[CHB][hapmap]
rs13094915	0.90[CHB][hapmap]
rs13303	0.90[CHB][hapmap]
rs1561337	0.84[CHB][hapmap]
rs17052256	0.84[CHB][hapmap]
rs17052259	0.85[CHB][hapmap]
rs17264436	0.85[CHB][hapmap]
rs1866268	0.84[CHB][hapmap]
rs1961959	0.90[CHB][hapmap]
rs2015971	0.81[CHB][hapmap];0.93[ASN][1000 genomes]
rs2028216	0.84[CHB][hapmap]
rs2083180	0.84[CHB][hapmap]
rs2118540	0.81[CHB][hapmap]
rs2164884	0.84[CHB][hapmap]
rs2164885	0.83[CHB][hapmap]
rs2251219	0.84[CHB][hapmap]
rs2276824	0.85[CHB][hapmap]
rs2289247	0.84[CHB][hapmap]
rs2289249	0.84[CHB][hapmap]
rs2289250	0.84[CHB][hapmap]
rs2336146	0.84[CHB][hapmap]
rs2336149	0.84[CHB][hapmap]
rs2577831	0.84[CHB][hapmap]
rs2590838	0.84[CHB][hapmap]
rs2878628	0.84[CHB][hapmap]
rs3199918	0.84[AFR][1000 genomes]
rs33967311	0.84[CHB][hapmap]
rs34736619	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3733039	0.84[CHB][hapmap]
rs3733041	0.84[CHB][hapmap]
rs3733045	0.84[CHB][hapmap]
rs3755806	0.84[CHB][hapmap]
rs3774365	0.85[CHB][hapmap]
rs3774366	0.84[CHB][hapmap]
rs3796353	0.84[CHB][hapmap]
rs3852066	0.84[CHB][hapmap]
rs4234633	0.85[ASN][1000 genomes]
rs4282054	0.90[CHB][hapmap]
rs4434138	0.84[ASN][1000 genomes]
rs4475032	0.90[CHB][hapmap]
rs4687548	0.85[CHB][hapmap]
rs4687624	0.85[ASN][1000 genomes]
rs4687625	0.89[CHB][hapmap]
rs4687626	0.90[CHB][hapmap]
rs4687629	0.85[CHB][hapmap]
rs4687638	0.84[CHB][hapmap]
rs6445528	0.90[CHB][hapmap]
rs6617	0.85[CHB][hapmap]
rs6762813	0.84[CHB][hapmap]
rs6778735	0.90[CHB][hapmap]
rs6778844	0.84[CHB][hapmap]
rs6786043	0.84[CHB][hapmap]
rs6786919	0.89[CHB][hapmap]
rs6798246	0.85[CHB][hapmap]
rs6804145	0.84[CHB][hapmap]
rs6805156	0.85[CHB][hapmap]
rs6976	0.84[CHB][hapmap]
rs731831	0.84[CHB][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611731	0.84[CHB][hapmap]
rs7614981	0.89[CHB][hapmap]
rs7622694	0.84[CHB][hapmap]
rs7638808	0.90[CHB][hapmap]
rs7652191	0.84[CHB][hapmap]
rs8906	0.84[CHB][hapmap]
rs9853056	1.00[CHB][hapmap]
rs9879090	0.90[CHB][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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590306	chr3:52536308-52557440	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1010552	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs1010552	PBRM1	cis	Artery Tibial	GTEx
rs1010552	PBRM1	cis	Thyroid	GTEx
rs1010552	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs1010552	FLJ12442	cis	multi-tissue	Pritchard
rs1010552	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs1010552	ITIH4-AS1	cis	Artery Aorta	GTEx
rs1010552	NT5DC2	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52513400-52541400	Weak transcription	A549	lung
2	chr3:52530200-52551800	Weak transcription	Esophagus	oesophagus
3	chr3:52530400-52552400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:52530800-52548200	Weak transcription	Right Ventricle	heart
6	chr3:52530800-52551600	Weak transcription	Fetal Intestine Small	intestine
7	chr3:52531000-52547600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:52533400-52540800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:52533400-52549200	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:52533400-52549200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:52533400-52558200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:52533400-52559800	Weak transcription	Liver	Liver
13	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:52535600-52541600	Strong transcription	Lung	lung
16	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:52536800-52542000	Weak transcription	Fetal Stomach	stomach
19	chr3:52536800-52552600	Strong transcription	Adipose Nuclei	Adipose
20	chr3:52537400-52541000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
21	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:52538400-52548200	Weak transcription	Colonic Mucosa	Colon
23	chr3:52538800-52540800	Strong transcription	Gastric	stomach
24	chr3:52538800-52544200	Weak transcription	Pancreas	Pancrea
25	chr3:52539000-52540600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:52539000-52546000	Strong transcription	Spleen	Spleen
27	chr3:52539800-52541600	Genic enhancers	HUVEC	blood vessel
28	chr3:52540000-52541200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:52540000-52553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:52540200-52540800	Bivalent Enhancer	HepG2	liver
31	chr3:52540200-52541000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:52540400-52540600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:52540400-52540600	Enhancers	NH-A	brain
34	chr3:52540400-52541000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:52540400-52541000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:52540400-52541200	Enhancers	Fetal Muscle Trunk	muscle
37	chr3:52540400-52541600	Weak transcription	Thymus	Thymus
38	chr3:52540400-52541800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:52540400-52542000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:52540400-52542200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:52540400-52542200	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links