Variant report

Variant	rs4884452
Chromosome Location	chr13:52949784-52949785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1056335	0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11148252	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11618716	0.91[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs11620062	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1327323	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs13431	0.87[ASN][1000 genomes]
rs1815348	0.86[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap]
rs1815669	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3803262	0.84[ASN][1000 genomes]
rs3803264	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3886077	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3892337	0.86[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap]
rs4286007	0.91[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4545703	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs4884320	0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4884354	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4885953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886018	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886077	0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs61958050	0.87[ASN][1000 genomes]
rs6561665	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.83[ASN][1000 genomes]
rs7321964	0.86[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs7323666	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7333451	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs7336679	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7399631	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7981050	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs7981732	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7983971	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs7985262	0.87[ASN][1000 genomes]
rs7987115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7990581	0.91[ASW][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.94[YRI][hapmap]
rs7993748	0.91[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8001624	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9379	0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs9526913	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526914	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535895	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs9535914	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs9536046	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536048	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9536052	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536066	0.91[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9536069	0.84[ASN][1000 genomes]
rs9536079	0.90[ASW][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.94[YRI][hapmap]
rs9536104	0.83[LWK][hapmap]
rs9568728	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568732	0.91[ASW][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs9568734	0.91[ASW][hapmap];0.80[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap]
rs9596643	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9596648	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9596649	0.80[EUR][1000 genomes]
rs9596651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4884452	CKAP2	cis	Artery Tibial	GTEx
rs4884452	CKAP2	cis	parietal	SCAN
rs4884452	VPS36	cis	cerebellum	SCAN
rs4884452	CKAP2	cis	Thyroid	GTEx
rs4884452	CKAP2	cis	multi-tissue	Pritchard
rs4884452	LECT1	cis	parietal	SCAN
rs4884452	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs4884452	HNRNPA1L2	cis	cerebellum	SCAN
rs4884452	CKAP2	cis	Nerve Tibial	GTEx
rs4884452	CKAP2	cis	Adipose Subcutaneous	GTEx
rs4884452	LOC440138	cis	multi-tissue	Pritchard
rs4884452	CKAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs4884452	CKAP2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52934000-52951800	Weak transcription	Fetal Intestine Small	intestine
2	chr13:52946000-52951800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:52946000-52951800	Weak transcription	Adipose Nuclei	Adipose
4	chr13:52946000-52951800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr13:52946000-52951800	Weak transcription	Left Ventricle	heart
6	chr13:52946000-52951800	Weak transcription	Lung	lung
7	chr13:52946000-52951800	Weak transcription	Pancreas	Pancrea
8	chr13:52946000-52951800	Weak transcription	Right Ventricle	heart
9	chr13:52946000-52952000	Weak transcription	Aorta	Aorta
10	chr13:52946000-52952000	Weak transcription	Ovary	ovary
11	chr13:52946000-52952800	Weak transcription	Gastric	stomach
12	chr13:52946000-52969600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr13:52946200-52951800	Weak transcription	Esophagus	oesophagus
14	chr13:52946200-52951800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr13:52946200-52952000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:52946200-52952600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr13:52946200-52979200	Weak transcription	A549	lung
18	chr13:52946800-52951800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:52946800-52951800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:52946800-52951800	Weak transcription	Fetal Muscle Leg	muscle
21	chr13:52947400-52951800	Weak transcription	NHLF	lung
22	chr13:52947600-52951800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr13:52947800-52950600	Weak transcription	HSMMtube	muscle
24	chr13:52947800-52968000	Weak transcription	NHDF-Ad	bronchial
25	chr13:52948000-52951800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:52948000-52952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr13:52948000-52952000	Weak transcription	NHEK	skin
28	chr13:52948600-52949800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:52948600-52950800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr13:52949000-52955800	Weak transcription	Brain Angular Gyrus	brain
31	chr13:52949200-52951800	Weak transcription	Brain Germinal Matrix	brain
32	chr13:52949400-52949800	Strong transcription	HSMM	muscle
33	chr13:52949400-52951800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr13:52949400-52951800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr13:52949400-52952000	Weak transcription	HMEC	breast
36	chr13:52949400-52952000	Weak transcription	HUVEC	blood vessel
37	chr13:52949600-52949800	Enhancers	Spleen	Spleen
38	chr13:52949600-52950600	Weak transcription	Osteobl	bone
39	chr13:52949600-52951400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr13:52949600-52951600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:52949600-52951800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr13:52949600-52952800	Weak transcription	Liver	Liver

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