Variant report

Variant	rs28393037
Chromosome Location	chr13:52723369-52723370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11616964	0.85[ASN][1000 genomes]
rs12584961	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1571189	0.81[EUR][1000 genomes]
rs1886542	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1886547	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1998696	0.90[ASN][1000 genomes]
rs2004866	0.85[ASN][1000 genomes]
rs2274202	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296348	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296349	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296350	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408544	0.87[ASN][1000 genomes]
rs2408549	0.94[ASN][1000 genomes]
rs2408550	0.94[ASN][1000 genomes]
rs2408551	0.94[ASN][1000 genomes]
rs2408609	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408611	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897976	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897977	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3368	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35895576	0.87[ASN][1000 genomes]
rs3825528	0.89[ASN][1000 genomes]
rs4297592	0.94[ASN][1000 genomes]
rs4941727	0.82[EUR][1000 genomes]
rs55772266	0.94[ASN][1000 genomes]
rs61958812	0.94[ASN][1000 genomes]
rs6650383	0.89[ASN][1000 genomes]
rs66849828	0.82[EUR][1000 genomes]
rs723102	0.92[ASN][1000 genomes]
rs723103	0.92[ASN][1000 genomes]
rs7327634	0.83[ASN][1000 genomes]
rs7337430	0.87[ASN][1000 genomes]
rs755363	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7993492	0.80[ASN][1000 genomes]
rs7995946	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9526821	0.83[ASN][1000 genomes]
rs9526832	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9526837	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526842	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535829	0.83[ASN][1000 genomes]
rs9535832	0.80[ASN][1000 genomes]
rs9535833	0.85[ASN][1000 genomes]
rs9535836	0.90[ASN][1000 genomes]
rs9535849	0.90[ASN][1000 genomes]
rs9535851	0.94[ASN][1000 genomes]
rs9535858	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9535860	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9535862	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9535866	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9535872	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9535878	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535879	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535880	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535882	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535883	0.86[EUR][1000 genomes]
rs9535885	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535887	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9563084	0.85[ASN][1000 genomes]
rs9563089	0.89[ASN][1000 genomes]
rs9563091	0.93[ASN][1000 genomes]
rs9563093	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568693	0.90[ASN][1000 genomes]
rs9568695	0.91[ASN][1000 genomes]
rs9568708	0.93[ASN][1000 genomes]
rs9568713	0.87[AFR][1000 genomes];0.99[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	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	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
4	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
5	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
6	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
rs28393037	CKAP2	cis	Nerve Tibial	GTEx
rs28393037	NEK3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52703600-52725200	Weak transcription	Right Ventricle	heart
2	chr13:52703600-52725200	Weak transcription	Small Intestine	intestine
3	chr13:52703600-52725600	Weak transcription	Fetal Brain Male	brain
4	chr13:52703600-52730800	Weak transcription	Stomach Mucosa	stomach
5	chr13:52703600-52731000	Weak transcription	Brain Angular Gyrus	brain
6	chr13:52703600-52732600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr13:52703600-52732800	Weak transcription	Psoas Muscle	Psoas
8	chr13:52703600-52733000	Weak transcription	Esophagus	oesophagus
9	chr13:52703800-52723800	Weak transcription	Colonic Mucosa	Colon
10	chr13:52703800-52724800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr13:52703800-52731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:52703800-52731400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr13:52703800-52731400	Weak transcription	Spleen	Spleen
14	chr13:52703800-52732600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr13:52703800-52732600	Weak transcription	HMEC	breast
16	chr13:52703800-52733200	Weak transcription	Gastric	stomach
17	chr13:52704000-52733000	Weak transcription	Fetal Thymus	thymus
18	chr13:52704200-52725400	Weak transcription	Primary T cells from cord blood	blood
19	chr13:52704800-52727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr13:52704800-52730000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr13:52706200-52731000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr13:52706600-52730800	Weak transcription	HUVEC	blood vessel
23	chr13:52706600-52731000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr13:52706600-52732600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr13:52706600-52732800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:52706600-52732800	Weak transcription	Pancreas	Pancrea
27	chr13:52707200-52725200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr13:52707400-52724800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr13:52707400-52725000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr13:52707400-52725200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr13:52707400-52725600	Weak transcription	Fetal Heart	heart
32	chr13:52707400-52731200	Weak transcription	Primary B cells from cord blood	blood
33	chr13:52707400-52732800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr13:52707600-52731600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr13:52707600-52732600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr13:52707800-52724600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr13:52707800-52732600	Weak transcription	A549	lung
38	chr13:52708000-52725400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr13:52708000-52732600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:52708200-52724600	Weak transcription	NH-A	brain
41	chr13:52708200-52725200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr13:52708200-52725200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr13:52708200-52725600	Weak transcription	NHLF	lung
44	chr13:52708400-52732600	Weak transcription	HSMMtube	muscle
45	chr13:52708400-52732800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr13:52710000-52725200	Weak transcription	Left Ventricle	heart
47	chr13:52710400-52724200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr13:52710400-52724800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr13:52710400-52724800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr13:52710400-52725000	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links