Variant report

Variant	rs4941727
Chromosome Location	chr13:52721067-52721068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1004576	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[ASN][1000 genomes]
rs1055062	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1060631	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1134727	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11620583	0.87[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap]
rs12146904	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12431310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12560598	0.84[ASN][1000 genomes]
rs1571189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1801243	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1886538	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs1886539	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1886542	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1886543	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1886544	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1886545	0.86[ASN][1000 genomes]
rs1886546	0.85[ASN][1000 genomes]
rs1886547	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1924611	0.86[CHB][hapmap]
rs2004866	0.91[CHB][hapmap]
rs2005182	0.92[ASN][1000 genomes]
rs2181891	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs2274202	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2277448	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2296347	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296348	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2296349	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2296350	0.83[EUR][1000 genomes]
rs2408544	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2408546	0.88[ASN][1000 genomes]
rs2408547	0.90[ASN][1000 genomes]
rs2408548	0.90[ASN][1000 genomes]
rs2408550	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2408551	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2408552	0.80[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.96[ASN][1000 genomes]
rs2408554	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2408609	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2408611	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs28393037	0.82[EUR][1000 genomes]
rs2897964	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2897965	0.99[ASN][1000 genomes]
rs2897976	0.83[EUR][1000 genomes]
rs2897977	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs3368	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs3742289	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3742291	0.85[ASN][1000 genomes]
rs3783242	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818422	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3825528	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4261421	0.88[ASN][1000 genomes]
rs4264295	0.89[ASN][1000 genomes]
rs4297592	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4497567	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs4545703	0.81[GIH][hapmap]
rs4943060	0.84[ASN][1000 genomes]
rs61958804	0.86[ASN][1000 genomes]
rs61958805	0.82[ASN][1000 genomes]
rs6561656	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6561658	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6650384	0.90[ASN][1000 genomes]
rs6650385	0.90[ASN][1000 genomes]
rs66849828	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7318287	0.89[ASN][1000 genomes]
rs7319784	0.82[ASN][1000 genomes]
rs7320252	0.90[ASN][1000 genomes]
rs7320429	0.90[ASN][1000 genomes]
rs732071	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs7320831	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7321120	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7321310	0.82[ASN][1000 genomes]
rs7321435	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs7324458	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7327634	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7332356	0.94[ASN][1000 genomes]
rs7338131	0.90[ASN][1000 genomes]
rs747781	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs755363	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7981904	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7991237	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7995946	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7998770	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9316563	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs9526819	0.87[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap]
rs9526823	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9526825	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9526826	0.90[ASN][1000 genomes]
rs9526834	0.91[ASN][1000 genomes]
rs9526835	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9526836	0.94[ASN][1000 genomes]
rs9526837	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9526841	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9526842	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9526843	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535812	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs9535822	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs9535825	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs9535826	0.87[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap]
rs9535832	0.91[CHB][hapmap]
rs9535836	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9535845	0.90[ASN][1000 genomes]
rs9535851	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9535853	0.94[ASN][1000 genomes]
rs9535856	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9535858	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9535861	0.80[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];0.88[ASN][1000 genomes]
rs9535862	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9535866	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9535867	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9535871	0.99[ASN][1000 genomes]
rs9535873	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[ASN][1000 genomes]
rs9535878	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9535879	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs9535880	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9535882	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9535883	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535885	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9535887	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9535888	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535889	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9563089	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9563093	0.82[EUR][1000 genomes]
rs9568682	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs9568684	0.84[JPT][hapmap]
rs9568692	0.90[ASN][1000 genomes]
rs9568713	0.91[CHB][hapmap];0.86[JPT][hapmap]

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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4941727	NEK3	cis	normal skin	skin_eQTL
rs4941727	CKAP2	cis	cerebellum	SCAN
rs4941727	LOC440138	cis	multi-tissue	Pritchard
rs4941727	NEK3	cis	Liver	GTEx
rs4941727	CKAP2	cis	multi-tissue	Pritchard
rs4941727	NEK3	cis	multi-tissue	Pritchard
rs4941727	NEK3	cis	Adipose Subcutaneous	GTEx
rs4941727	CKAP2	cis	Nerve Tibial	GTEx
rs4941727	NEK3	cis	Muscle Skeletal	GTEx
rs4941727	VPS36	cis	cerebellum	SCAN
rs4941727	CKAP2	cis	Artery Tibial	GTEx
rs4941727	CKAP2	cis	parietal	SCAN

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	chr13:52706600-52721400	Weak transcription	NHEK	skin
23	chr13:52706600-52730800	Weak transcription	HUVEC	blood vessel
24	chr13:52706600-52731000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:52706600-52732600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr13:52706600-52732800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:52706600-52732800	Weak transcription	Pancreas	Pancrea
28	chr13:52707200-52725200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:52707400-52721400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr13:52707400-52724800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr13:52707400-52725000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr13:52707400-52725200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr13:52707400-52725600	Weak transcription	Fetal Heart	heart
34	chr13:52707400-52731200	Weak transcription	Primary B cells from cord blood	blood
35	chr13:52707400-52732800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr13:52707600-52731600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr13:52707600-52732600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:52707800-52724600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr13:52707800-52732600	Weak transcription	A549	lung
40	chr13:52708000-52725400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr13:52708000-52732600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr13:52708200-52724600	Weak transcription	NH-A	brain
43	chr13:52708200-52725200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr13:52708200-52725200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr13:52708200-52725600	Weak transcription	NHLF	lung
46	chr13:52708400-52722400	Weak transcription	Fetal Kidney	kidney
47	chr13:52708400-52732600	Weak transcription	HSMMtube	muscle
48	chr13:52708400-52732800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr13:52710000-52725200	Weak transcription	Left Ventricle	heart
50	chr13:52710400-52724200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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