Variant report

Variant	rs3783240
Chromosome Location	chr13:52516230-52516231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52515170..52518046-chr13:52524661..52527168,2	MCF-7	breast:
2	chr13:52515307..52517752-chr13:52524777..52526325,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1004576	0.87[CEU][hapmap]
rs1051332	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1061472	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1801249	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1886538	0.91[CEU][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1924608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1924609	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1924619	0.99[ASN][1000 genomes]
rs1998611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2031992	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2104353	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2147359	0.81[EUR][1000 genomes]
rs2147360	0.81[EUR][1000 genomes]
rs2147363	0.88[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2282057	0.96[ASN][1000 genomes]
rs2282058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2296246	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2408510	0.95[ASN][1000 genomes]
rs2408554	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs3825526	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4941720	0.81[EUR][1000 genomes]
rs4943044	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4943045	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4943046	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4943048	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7139967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7140038	0.99[ASN][1000 genomes]
rs732071	0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs7321435	0.82[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs7321445	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7321909	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs732774	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7328751	0.82[ASN][1000 genomes]
rs752569	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs754609	0.96[ASN][1000 genomes]
rs754610	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7998770	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs928169	0.97[ASN][1000 genomes]
rs9316562	0.94[ASN][1000 genomes]
rs942463	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9526812	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9526814	0.85[CHB][hapmap]
rs9526817	0.81[EUR][1000 genomes]
rs9535792	0.97[ASN][1000 genomes]
rs9535793	0.97[ASN][1000 genomes]
rs9535795	0.97[ASN][1000 genomes]
rs9535796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9535816	0.81[EUR][1000 genomes]
rs9535821	0.80[EUR][1000 genomes]
rs9535824	0.81[EUR][1000 genomes]
rs9535873	0.87[CEU][hapmap]
rs9563078	0.81[JPT][hapmap]
rs9568677	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9568682	0.82[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs9568684	0.81[EUR][1000 genomes]
rs9591439	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3783240	CKAP2	cis	parietal	SCAN
rs3783240	NCRNA00282	cis	cerebellum	SCAN
rs3783240	NEK5	cis	cerebellum	SCAN
rs3783240	ATP7B	cis	lymphoblastoid	seeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52486400-52523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
4	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr13:52494800-52527000	Weak transcription	Fetal Lung	lung
6	chr13:52496600-52524200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:52497600-52519600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr13:52501600-52532400	Strong transcription	HepG2	liver
10	chr13:52502800-52518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:52502800-52529200	Weak transcription	Psoas Muscle	Psoas
12	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr13:52505600-52520800	Strong transcription	Fetal Intestine Small	intestine
15	chr13:52505600-52531800	Strong transcription	Liver	Liver
16	chr13:52505800-52527200	Strong transcription	Fetal Intestine Large	intestine
17	chr13:52506000-52517200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr13:52506000-52520800	Strong transcription	Adipose Nuclei	Adipose
19	chr13:52506000-52527200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr13:52506800-52524400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr13:52507000-52517200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr13:52507400-52517400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr13:52507400-52518400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr13:52508000-52532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr13:52509000-52518200	Weak transcription	Esophagus	oesophagus
26	chr13:52509000-52530000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
28	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:52509600-52518600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr13:52509800-52529600	Weak transcription	Small Intestine	intestine
32	chr13:52510000-52518600	Weak transcription	Spleen	Spleen
33	chr13:52511400-52520600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr13:52511400-52520600	Strong transcription	Right Ventricle	heart
35	chr13:52511800-52535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:52512600-52516400	Weak transcription	Gastric	stomach
37	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
38	chr13:52512800-52518000	Weak transcription	Fetal Brain Female	brain
39	chr13:52513200-52518000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
41	chr13:52513400-52516400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr13:52513400-52517200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:52513400-52542000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
45	chr13:52513600-52516400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:52514600-52520600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr13:52514600-52521000	Strong transcription	Fetal Muscle Leg	muscle
48	chr13:52514800-52516400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr13:52514800-52516800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr13:52514800-52518200	Strong transcription	Fetal Muscle Trunk	muscle

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