Variant report

Variant	rs7321445
Chromosome Location	chr13:52526612-52526613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52525579..52528317-chr13:52530342..52532434,2	K562	blood:
2	chr13:52515170..52518046-chr13:52524661..52527168,2	MCF-7	breast:
3	chr13:52525725..52527741-chr13:52584765..52586393,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1801249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1924608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924619	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1998611	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2031992	0.88[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2104353	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2282057	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296246	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2408510	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3783240	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[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];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943048	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]
rs7139967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7140038	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7321909	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732774	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7328751	0.81[CEU][hapmap]
rs752569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs754609	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs754610	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs928169	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316562	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs942463	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526812	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9526814	0.85[CHB][hapmap]
rs9535792	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535793	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535795	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9563078	0.81[JPT][hapmap]
rs9568677	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9591439	0.81[EUR][1000 genomes];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7321445	CKAP2	cis	parietal	SCAN
rs7321445	ATP7B	cis	cerebellum	SCAN
rs7321445	NCRNA00282	cis	cerebellum	SCAN

Chromatin state (count:76 , 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	chr13:52494800-52527000	Weak transcription	Fetal Lung	lung
5	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr13:52501600-52532400	Strong transcription	HepG2	liver
7	chr13:52502800-52529200	Weak transcription	Psoas Muscle	Psoas
8	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:52505600-52531800	Strong transcription	Liver	Liver
11	chr13:52505800-52527200	Strong transcription	Fetal Intestine Large	intestine
12	chr13:52506000-52527200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr13:52508000-52532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:52509000-52530000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
16	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:52509800-52529600	Weak transcription	Small Intestine	intestine
19	chr13:52511800-52535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
21	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
22	chr13:52513400-52542000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:52516000-52531800	Weak transcription	Fetal Kidney	kidney
25	chr13:52516000-52548000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:52516800-52529200	Weak transcription	Pancreas	Pancrea
28	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr13:52518400-52529200	Weak transcription	Colonic Mucosa	Colon
30	chr13:52518600-52528600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr13:52518600-52528600	Weak transcription	Stomach Mucosa	stomach
32	chr13:52518800-52527600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr13:52519400-52546000	Weak transcription	Spleen	Spleen
34	chr13:52520200-52529400	Weak transcription	Gastric	stomach
35	chr13:52520600-52528200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr13:52520600-52528400	Weak transcription	Right Ventricle	heart
37	chr13:52520600-52553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr13:52520800-52529000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr13:52520800-52531400	Weak transcription	Brain Anterior Caudate	brain
40	chr13:52523800-52532800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr13:52524200-52527800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr13:52524600-52528000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr13:52524600-52528400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr13:52524600-52528400	Weak transcription	Left Ventricle	heart
45	chr13:52524800-52528200	Weak transcription	Fetal Muscle Leg	muscle
46	chr13:52524800-52528200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr13:52524800-52528600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr13:52524800-52528600	Weak transcription	K562	blood
49	chr13:52524800-52528800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr13:52524800-52529400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links