Variant report

Variant	rs3368
Chromosome Location	chr13:52707240-52707241
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr13:52707106-52707380	K562	blood:	n/a	n/a

Variant related genes	Relation type
NEK5	TF binding region

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1004576	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1055062	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1060631	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs11616964	0.85[ASN][1000 genomes]
rs11620583	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap]
rs12146904	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs12431310	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12584961	0.85[ASN][1000 genomes]
rs1571189	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs1801243	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1886538	0.81[CHB][hapmap]
rs1886542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886543	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886544	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1886547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[ASN][1000 genomes]
rs1924611	0.87[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs1998696	0.91[ASN][1000 genomes]
rs2004866	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs2181891	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2274202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277448	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2296347	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2296348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296350	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs2408549	0.94[ASN][1000 genomes]
rs2408550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[ASN][1000 genomes]
rs2408551	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2408552	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2408554	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393037	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897964	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2897976	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35895576	0.87[ASN][1000 genomes]
rs3742289	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3783242	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3818422	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3825528	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[ASN][1000 genomes]
rs4297592	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[ASN][1000 genomes]
rs4497567	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4941727	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs55772266	0.94[ASN][1000 genomes]
rs61958812	0.94[ASN][1000 genomes]
rs6561656	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs6561658	0.89[CEU][hapmap]
rs6650383	0.90[ASN][1000 genomes]
rs66849828	0.82[EUR][1000 genomes]
rs723102	0.93[ASN][1000 genomes]
rs723103	0.93[ASN][1000 genomes]
rs732071	0.81[CHB][hapmap]
rs7320831	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7321120	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7321435	0.81[CHB][hapmap]
rs7324458	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7327634	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs7337430	0.87[ASN][1000 genomes]
rs747781	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs755363	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7981904	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs7991237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7993492	0.81[ASN][1000 genomes]
rs7995946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7998770	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9316563	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap]
rs9526819	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs9526821	0.84[ASN][1000 genomes]
rs9526823	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526825	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526832	0.89[ASN][1000 genomes]
rs9526837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526841	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs9526842	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535812	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9535822	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs9535825	0.81[CHB][hapmap]
rs9535826	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs9535828	0.89[YRI][hapmap]
rs9535829	0.84[ASN][1000 genomes]
rs9535832	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9535833	0.85[ASN][1000 genomes]
rs9535836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[ASN][1000 genomes]
rs9535849	0.91[ASN][1000 genomes]
rs9535851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[ASN][1000 genomes]
rs9535856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs9535858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[ASN][1000 genomes]
rs9535860	0.96[ASN][1000 genomes]
rs9535861	0.82[CHB][hapmap]
rs9535862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs9535866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9535867	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535872	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535873	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535883	0.85[EUR][1000 genomes]
rs9535885	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9563084	0.86[ASN][1000 genomes]
rs9563089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[ASN][1000 genomes]
rs9563091	0.93[ASN][1000 genomes]
rs9563093	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568682	0.81[CHB][hapmap]
rs9568693	0.91[ASN][1000 genomes]
rs9568695	0.92[ASN][1000 genomes]
rs9568708	0.93[ASN][1000 genomes]
rs9568713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.99[ASN][1000 genomes]

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	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
3	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
4	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
5	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
6	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3368	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs3368	CKAP2	cis	Nerve Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52703600-52709600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr13:52703600-52720400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr13:52703600-52725200	Weak transcription	Right Ventricle	heart
4	chr13:52703600-52725200	Weak transcription	Small Intestine	intestine
5	chr13:52703600-52725600	Weak transcription	Fetal Brain Male	brain
6	chr13:52703600-52730800	Weak transcription	Stomach Mucosa	stomach
7	chr13:52703600-52731000	Weak transcription	Brain Angular Gyrus	brain
8	chr13:52703600-52732600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr13:52703600-52732800	Weak transcription	Psoas Muscle	Psoas
10	chr13:52703600-52733000	Weak transcription	Esophagus	oesophagus
11	chr13:52703800-52709000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:52703800-52720000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr13:52703800-52720400	Weak transcription	HSMM	muscle
14	chr13:52703800-52723800	Weak transcription	Colonic Mucosa	Colon
15	chr13:52703800-52724800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr13:52703800-52731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:52703800-52731400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr13:52703800-52731400	Weak transcription	Spleen	Spleen
19	chr13:52703800-52732600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr13:52703800-52732600	Weak transcription	HMEC	breast
21	chr13:52703800-52733200	Weak transcription	Gastric	stomach
22	chr13:52704000-52711000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:52704000-52733000	Weak transcription	Fetal Thymus	thymus
24	chr13:52704200-52708800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr13:52704200-52709600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr13:52704200-52709600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr13:52704200-52725400	Weak transcription	Primary T cells from cord blood	blood
28	chr13:52704600-52707400	Strong transcription	Fetal Heart	heart
29	chr13:52704800-52708000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr13:52704800-52710400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr13:52704800-52727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr13:52704800-52730000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr13:52705000-52707800	Strong transcription	A549	lung
34	chr13:52705000-52708400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:52705000-52710400	Strong transcription	Brain Germinal Matrix	brain
36	chr13:52705000-52711000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr13:52705000-52711200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:52705000-52712400	Strong transcription	HepG2	liver
39	chr13:52705000-52716200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr13:52705200-52707800	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr13:52705200-52708200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr13:52705200-52708200	Strong transcription	Liver	Liver
43	chr13:52705200-52708400	Strong transcription	Fetal Brain Female	brain
44	chr13:52705200-52708400	Strong transcription	Fetal Lung	lung
45	chr13:52705200-52708400	Strong transcription	HSMMtube	muscle
46	chr13:52705200-52709000	Strong transcription	Brain Substantia Nigra	brain
47	chr13:52705200-52709000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr13:52705200-52709200	Strong transcription	Left Ventricle	heart
49	chr13:52705200-52710400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:52705200-52710400	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links