Variant report

Variant	rs9596648
Chromosome Location	chr13:52934569-52934570
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1056335	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11148252	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11618716	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11620062	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1327323	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs13431	0.85[ASN][1000 genomes]
rs1815348	0.90[CHB][hapmap]
rs1815669	0.85[ASN][1000 genomes]
rs3803262	0.82[ASN][1000 genomes]
rs3803264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3886077	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs3892337	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4286007	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4545703	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4884320	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4884354	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4884452	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4885953	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4886018	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4886077	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs61958050	0.85[ASN][1000 genomes]
rs6561665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7321964	0.86[CHB][hapmap]
rs7323666	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7333451	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7336679	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7399631	0.82[ASN][1000 genomes]
rs7981050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7981732	0.82[ASN][1000 genomes]
rs7983971	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7985262	0.85[ASN][1000 genomes]
rs7987115	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7990581	0.86[CHB][hapmap]
rs7993748	0.90[CHB][hapmap]
rs8001624	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9379	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9526913	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9526914	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535895	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9535914	0.83[CEU][hapmap]
rs9536046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9536048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9536052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9536066	0.86[CHB][hapmap]
rs9536069	0.82[ASN][1000 genomes]
rs9536079	0.86[CHB][hapmap]
rs9568728	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568732	0.86[CHB][hapmap]
rs9568734	0.80[CHB][hapmap]
rs9596643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9596651	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[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	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
6	nsv977385	chr13:52918841-52936623	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9596648	CKAP2	cis	Artery Tibial	GTEx
rs9596648	CKAP2	cis	Nerve Tibial	GTEx
rs9596648	CKAP2	cis	Adipose Subcutaneous	GTEx
rs9596648	CKAP2	cis	Thyroid	GTEx
rs9596648	NEK3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52931000-52935400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:52931200-52935200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:52931400-52935200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:52931400-52935200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr13:52931400-52935400	Weak transcription	HMEC	breast
6	chr13:52931400-52935400	Weak transcription	NHEK	skin
7	chr13:52931400-52935600	Weak transcription	Osteobl	bone
8	chr13:52931400-52937200	Weak transcription	NH-A	brain
9	chr13:52932800-52934800	Enhancers	Fetal Muscle Leg	muscle
10	chr13:52933200-52934600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:52934000-52951800	Weak transcription	Fetal Intestine Small	intestine
12	chr13:52934400-52940400	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links