Variant report

Variant	rs4943048
Chromosome Location	chr13:52530522-52530523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52521155..52523610-chr13:52530380..52532308,2	MCF-7	breast:
2	chr13:52525579..52528317-chr13:52530342..52532434,2	K562	blood:
3	chr13:52522149..52524363-chr13:52528676..52530661,2	K562	blood:
4	chr13:52530274..52531929-chr13:52534277..52536786,2	MCF-7	breast:
5	chr13:52526952..52529945-chr13:52530392..52532548,2	MCF-7	breast:
6	chr13:52528654..52531315-chr13:52532964..52534953,3	K562	blood:
7	chr13:52528629..52531468-chr13:52535704..52537368,2	K562	blood:

Variant related genes	Relation type
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1051332	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1061472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1801249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1924608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1924609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1924619	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1998611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031992	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.85[EUR][1000 genomes]
rs2104353	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2282057	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296246	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2408510	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3783240	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3825526	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4943044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7139967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7140038	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7321445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7321909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7328751	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs752569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754609	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754610	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs928169	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316562	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs942463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526812	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9526814	0.85[CHB][hapmap]
rs9535792	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535793	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535795	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9563078	0.81[JPT][hapmap]
rs9568677	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9591439	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4943048	THSD1	cis	cerebellum	SCAN
rs4943048	NEK5	cis	cerebellum	SCAN
rs4943048	CKAP2	cis	cerebellum	SCAN
rs4943048	CKAP2	cis	parietal	SCAN
rs4943048	LOC440138	cis	multi-tissue	Pritchard
rs4943048	ATP7B	cis	cerebellum	SCAN
rs4943048	NCRNA00282	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
3	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr13:52501600-52532400	Strong transcription	HepG2	liver
6	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:52505600-52531800	Strong transcription	Liver	Liver
9	chr13:52508000-52532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
11	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr13:52511800-52535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
15	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
16	chr13:52513400-52542000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
18	chr13:52516000-52531800	Weak transcription	Fetal Kidney	kidney
19	chr13:52516000-52548000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr13:52519400-52546000	Weak transcription	Spleen	Spleen
23	chr13:52520600-52553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr13:52520800-52531400	Weak transcription	Brain Anterior Caudate	brain
25	chr13:52523800-52532800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr13:52525200-52531400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr13:52525200-52550200	Weak transcription	Fetal Brain Female	brain
28	chr13:52525400-52531400	Strong transcription	Fetal Intestine Small	intestine
29	chr13:52525400-52553000	Weak transcription	Ovary	ovary
30	chr13:52527000-52530800	Enhancers	Fetal Lung	lung
31	chr13:52528000-52530800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:52528000-52543200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr13:52528200-52530800	Enhancers	Fetal Muscle Trunk	muscle
34	chr13:52528200-52532600	Enhancers	Fetal Muscle Leg	muscle
35	chr13:52528200-52532800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr13:52528200-52536000	Strong transcription	Adipose Nuclei	Adipose
37	chr13:52528400-52531200	Strong transcription	Fetal Stomach	stomach
38	chr13:52528400-52540800	Weak transcription	Lung	lung
39	chr13:52528400-52544000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr13:52528600-52531200	Strong transcription	Fetal Intestine Large	intestine
41	chr13:52528600-52534000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr13:52528600-52534000	Enhancers	Stomach Mucosa	stomach
43	chr13:52528600-52534200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr13:52528800-52542200	Weak transcription	Fetal Heart	heart
45	chr13:52529000-52531000	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr13:52529000-52531400	Weak transcription	Left Ventricle	heart
47	chr13:52529000-52532600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr13:52529200-52530600	Enhancers	Esophagus	oesophagus
49	chr13:52529200-52530800	Strong transcription	Pancreas	Pancrea
50	chr13:52529200-52531000	Enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links