Variant report

Variant	rs7321120
Chromosome Location	chr13:52584778-52584779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52584477..52586900-chr13:52700506..52703372,3	K562	blood:
2	chr13:52584551..52590049-chr13:52591418..52597330,6	K562	blood:
3	chr13:52584543..52591722-chr13:52593134..52598355,11	K562	blood:
4	chr13:52584477..52586943-chr13:52701489..52703372,3	K562	blood:

Variant related genes	Relation type
ENSG00000253710	Chromatin interaction
ENSG00000197168	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1004576	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs1055062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1060631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1134727	0.87[ASN][1000 genomes]
rs11620583	0.87[CHB][hapmap]
rs12146904	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs12431310	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12560598	0.87[ASN][1000 genomes]
rs1571189	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1801243	0.91[CHB][hapmap]
rs1886538	0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs1886539	0.85[ASN][1000 genomes]
rs1886542	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886543	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1886544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs1886545	0.88[ASN][1000 genomes]
rs1886546	0.88[ASN][1000 genomes]
rs1886547	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1924611	0.86[CHB][hapmap]
rs2004866	0.91[CHB][hapmap]
rs2005182	0.89[ASN][1000 genomes]
rs2147359	0.90[ASN][1000 genomes]
rs2147360	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2147361	0.87[ASN][1000 genomes]
rs2181891	0.91[CHB][hapmap]
rs2274202	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2277448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296347	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2296348	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2296349	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408544	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408546	0.91[ASN][1000 genomes]
rs2408547	0.92[ASN][1000 genomes]
rs2408548	0.92[ASN][1000 genomes]
rs2408550	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408551	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408552	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs2408554	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[ASN][1000 genomes]
rs2408609	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2408611	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2897964	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2897965	0.84[ASN][1000 genomes]
rs2897977	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3368	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3742289	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3742291	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3783242	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3818422	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3825528	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs4261421	0.91[ASN][1000 genomes]
rs4264295	0.92[ASN][1000 genomes]
rs4297592	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4497567	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs4600369	0.90[ASN][1000 genomes]
rs4941720	0.90[ASN][1000 genomes]
rs4941723	0.88[ASN][1000 genomes]
rs4941727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4943060	0.84[ASN][1000 genomes]
rs61958804	0.95[ASN][1000 genomes]
rs61958805	0.85[ASN][1000 genomes]
rs6561656	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6561658	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs6650384	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6650385	0.92[ASN][1000 genomes]
rs66849828	0.82[ASN][1000 genomes]
rs7318287	0.92[ASN][1000 genomes]
rs7319784	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320252	0.92[ASN][1000 genomes]
rs7320429	0.92[ASN][1000 genomes]
rs732071	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs7320831	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7321310	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321435	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7321775	0.90[ASN][1000 genomes]
rs7324458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7327634	0.91[CHB][hapmap]
rs7332272	0.85[ASN][1000 genomes]
rs7332356	0.88[ASN][1000 genomes]
rs7338131	0.92[ASN][1000 genomes]
rs747781	0.91[CHB][hapmap]
rs755363	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7981904	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7991237	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7995946	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7998770	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[ASN][1000 genomes]
rs9316563	0.87[CHB][hapmap]
rs9526817	0.90[ASN][1000 genomes]
rs9526819	0.87[CHB][hapmap]
rs9526823	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9526825	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9526826	0.92[ASN][1000 genomes]
rs9526834	0.91[ASN][1000 genomes]
rs9526835	0.84[ASN][1000 genomes]
rs9526836	0.88[ASN][1000 genomes]
rs9526837	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9526842	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9526843	0.85[ASN][1000 genomes]
rs9535812	0.91[CHB][hapmap]
rs9535813	0.90[ASN][1000 genomes]
rs9535816	0.91[ASN][1000 genomes]
rs9535821	0.89[ASN][1000 genomes]
rs9535822	0.86[CHB][hapmap]
rs9535824	0.91[ASN][1000 genomes]
rs9535825	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9535826	0.87[CHB][hapmap]
rs9535832	0.91[CHB][hapmap]
rs9535836	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535845	0.92[ASN][1000 genomes]
rs9535851	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535853	0.88[ASN][1000 genomes]
rs9535856	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535858	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535861	0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs9535862	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535866	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535867	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs9535871	0.83[ASN][1000 genomes]
rs9535873	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs9535878	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535879	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9535880	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535882	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535885	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9535887	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535889	0.81[ASN][1000 genomes]
rs9563089	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9568682	0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9568684	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs9568692	0.92[ASN][1000 genomes]
rs9568713	0.91[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7321120	NEK3	cis	parietal	SCAN
rs7321120	CKAP2	cis	cerebellum	SCAN
rs7321120	NEK3	cis	cerebellum	SCAN
rs7321120	VPS36	cis	cerebellum	SCAN
rs7321120	CKAP2	cis	parietal	SCAN
rs7321120	NEK5	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52570800-52585000	Weak transcription	Colonic Mucosa	Colon
2	chr13:52570800-52585200	Weak transcription	Aorta	Aorta
3	chr13:52574200-52585000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:52574400-52585000	Weak transcription	Left Ventricle	heart
5	chr13:52574400-52585200	Weak transcription	Lung	lung
6	chr13:52578400-52585200	Weak transcription	Pancreas	Pancrea
7	chr13:52579200-52585000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr13:52579200-52585000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr13:52579200-52585200	Weak transcription	Gastric	stomach
10	chr13:52579400-52585000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr13:52580600-52584800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr13:52580800-52585000	Weak transcription	Placenta	Placenta
13	chr13:52581000-52585200	Weak transcription	Spleen	Spleen
14	chr13:52581200-52585200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:52583600-52584800	Enhancers	Fetal Brain Male	brain
16	chr13:52583600-52584800	Enhancers	Fetal Intestine Large	intestine
17	chr13:52583600-52587400	Active TSS	Fetal Intestine Small	intestine
18	chr13:52583800-52585000	Enhancers	Brain Germinal Matrix	brain
19	chr13:52584000-52585000	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr13:52584200-52585000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr13:52584200-52585000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr13:52584200-52585000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:52584200-52585000	Enhancers	Colon Smooth Muscle	Colon
24	chr13:52584200-52585000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr13:52584200-52585200	Active TSS	Duodenum Mucosa	Duodenum
26	chr13:52584200-52585200	Weak transcription	Stomach Mucosa	stomach
27	chr13:52584200-52585600	Flanking Active TSS	Liver	Liver
28	chr13:52584200-52585800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr13:52584400-52584800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:52584400-52584800	Enhancers	Brain Hippocampus Middle	brain
31	chr13:52584400-52584800	Flanking Active TSS	K562	blood
32	chr13:52584400-52585000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:52584400-52585000	Active TSS	Fetal Stomach	stomach
34	chr13:52584400-52585200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:52584400-52585200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr13:52584400-52585400	Active TSS	HepG2	liver
37	chr13:52584400-52585600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:52584400-52587200	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr13:52584400-52587400	Active TSS	Brain Anterior Caudate	brain
40	chr13:52584400-52587400	Active TSS	Right Ventricle	heart
41	chr13:52584400-52587600	Active TSS	Right Atrium	heart
42	chr13:52584400-52587800	Active TSS	Brain Angular Gyrus	brain
43	chr13:52584600-52584800	Enhancers	Brain Substantia Nigra	brain
44	chr13:52584600-52584800	Bivalent/Poised TSS	NHDF-Ad	bronchial
45	chr13:52584600-52585000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
46	chr13:52584600-52585000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr13:52584600-52585000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr13:52584600-52585000	Enhancers	Adipose Nuclei	Adipose
49	chr13:52584600-52585000	Flanking Active TSS	Fetal Kidney	kidney
50	chr13:52584600-52585000	Enhancers	Pancreatic Islets	Pancreatic Islet

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