Variant report

Variant	rs1010553
Chromosome Location	chr3:52540773-52540774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000010327	Chromatin interaction
ENSG00000168273	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1010552	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs1010554	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10510760	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs10865973	0.82[CHB][hapmap]
rs10865974	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1108842	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11130306	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130310	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs11130312	0.82[CHB][hapmap]
rs11130315	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs11130317	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs11177	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1133415	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs11709284	0.84[EUR][1000 genomes]
rs11714419	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs11714565	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs11720159	0.82[CHB][hapmap]
rs11720243	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs12487445	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs12487591	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs12489828	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12496634	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs12635140	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs13063160	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs13064064	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs13068293	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs13081028	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13083798	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs13085895	0.82[CHB][hapmap]
rs13094915	0.91[CHB][hapmap]
rs13303	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[EUR][1000 genomes]
rs1561337	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs17052256	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs17052259	0.82[CHB][hapmap]
rs17264436	0.82[CHB][hapmap]
rs1866268	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1961958	0.81[CHD][hapmap]
rs1961959	0.82[CHB][hapmap]
rs2015971	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2028216	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2083180	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2164884	0.81[CHB][hapmap]
rs2164885	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs2251219	0.82[CHB][hapmap]
rs2276824	0.82[CHB][hapmap]
rs2289247	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2289249	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs2289250	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2336146	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2336149	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2577831	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs2590838	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs2878628	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs33967311	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs3733039	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs3733041	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs3733045	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs3755806	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs3774365	0.82[CHB][hapmap]
rs3774366	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs3796353	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs3852066	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs4282054	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[EUR][1000 genomes]
rs4475032	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs4687548	0.82[CHB][hapmap]
rs4687625	0.85[CHB][hapmap]
rs4687626	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs4687629	0.82[CHB][hapmap]
rs4687638	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs6445528	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs6617	0.82[CHB][hapmap]
rs66782572	0.82[EUR][1000 genomes]
rs66824127	0.87[EUR][1000 genomes]
rs67409736	0.82[EUR][1000 genomes]
rs6762813	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs6778735	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[EUR][1000 genomes]
rs6778844	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs6786043	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs6786919	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs6798246	0.82[CHB][hapmap]
rs6804145	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs6805156	0.82[CHB][hapmap]
rs6976	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs731831	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs7611731	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs7614981	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7622694	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs7636227	0.85[EUR][1000 genomes]
rs7638808	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs7652191	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs8906	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs9853056	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap]
rs9879090	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1010553	NEK4	cis	cerebellum	SCAN
rs1010553	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs1010553	NT5DC2	cis	multi-tissue	Pritchard
rs1010553	GLYCTK	cis	parietal	SCAN
rs1010553	RBM6	cis	cerebellum	SCAN
rs1010553	ITIH4	cis	lymphoblastoid	seeQTL
rs1010553	NT5DC2	cis	lymphoblastoid	seeQTL
rs1010553	NDUFAF3	cis	parietal	SCAN
rs1010553	FLJ12442	cis	multi-tissue	Pritchard
rs1010553	GNL3	cis	parietal	SCAN
rs1010553	SPCS1	cis	parietal	SCAN
rs1010553	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs1010553	SEMA3G	cis	parietal	SCAN
rs1010553	GNL3	cis	cerebellum	SCAN
rs1010553	NEK4	cis	parietal	SCAN
rs1010553	GLT8D1	cis	lymphoblastoid	seeQTL
rs1010553	RBM6	cis	parietal	SCAN
rs1010553	IL17RB	cis	parietal	SCAN

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	chr3:52539000-52546000	Strong transcription	Spleen	Spleen
26	chr3:52539800-52541600	Genic enhancers	HUVEC	blood vessel
27	chr3:52540000-52541200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:52540000-52553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:52540200-52540800	Bivalent Enhancer	HepG2	liver
30	chr3:52540200-52541000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:52540400-52541000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:52540400-52541000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:52540400-52541200	Enhancers	Fetal Muscle Trunk	muscle
34	chr3:52540400-52541600	Weak transcription	Thymus	Thymus
35	chr3:52540400-52541800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:52540400-52542000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:52540400-52542200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr3:52540400-52542200	Enhancers	Placenta	Placenta
39	chr3:52540600-52541000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:52540600-52541000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:52540600-52541400	Weak transcription	NH-A	brain

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