Variant report

Variant	rs6561666
Chromosome Location	chr13:52930045-52930046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1056335	0.90[CHB][hapmap]
rs11148252	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs11618716	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs11620062	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12430144	0.81[CHB][hapmap]
rs12870706	0.80[CHB][hapmap]
rs1327323	0.85[CHB][hapmap]
rs1815348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3803264	0.90[CHB][hapmap]
rs3886077	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs3892337	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4286007	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs4545703	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs4884320	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4884354	0.95[CHB][hapmap]
rs4884452	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap]
rs4885953	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs4886018	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs4886077	0.95[CHB][hapmap]
rs6561664	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6561665	0.90[CHB][hapmap]
rs7321964	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs7323666	0.95[CHB][hapmap]
rs7328653	0.87[ASN][1000 genomes]
rs7333451	0.95[CHB][hapmap]
rs7334583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336679	0.95[CHB][hapmap]
rs7400602	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7981050	0.90[CHB][hapmap]
rs7981732	0.83[EUR][1000 genomes]
rs7983971	0.90[CHB][hapmap]
rs7987115	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap]
rs7990581	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs7993748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8001624	0.95[CHB][hapmap]
rs9379	0.90[CHB][hapmap]
rs9526913	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs9526927	0.87[ASN][1000 genomes]
rs9535887	0.81[GIH][hapmap];0.91[MEX][hapmap]
rs9535895	0.82[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9535914	0.89[CEU][hapmap]
rs9536046	0.90[CHB][hapmap]
rs9536048	0.90[CHB][hapmap]
rs9536052	0.90[CHB][hapmap]
rs9536066	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9536079	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs9568732	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs9568734	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs9596643	0.89[CHB][hapmap]
rs9596648	0.90[CHB][hapmap]
rs9596649	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596651	0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[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	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6561666	LECT1	cis	parietal	SCAN
rs6561666	CKAP2	cis	multi-tissue	Pritchard
rs6561666	LOC440138	cis	multi-tissue	Pritchard
rs6561666	CKAP2	cis	Nerve Tibial	GTEx
rs6561666	CKAP2	cis	Adipose Subcutaneous	GTEx
rs6561666	CKAP2	cis	lung	GTEx
rs6561666	CKAP2	cis	parietal	SCAN
rs6561666	CKAP2	cis	Artery Tibial	GTEx
rs6561666	CKAP2	cis	cerebellum	SCAN
rs6561666	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs6561666	HNRNPA1L2	cis	cerebellum	SCAN
rs6561666	CKAP2	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52923600-52930200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:52927600-52930200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr13:52927600-52930600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:52927800-52930400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr13:52927800-52930400	Weak transcription	NHDF-Ad	bronchial
6	chr13:52928000-52933400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr13:52928400-52930400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:52928600-52930600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr13:52929000-52930200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:52929000-52930400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:52929400-52931200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:52929600-52931400	Enhancers	NH-A	brain
13	chr13:52929800-52931200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr13:52929800-52931400	Enhancers	HMEC	breast
15	chr13:52929800-52931400	Enhancers	Osteobl	bone
16	chr13:52930000-52930600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr13:52930000-52931000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr13:52930000-52931200	Enhancers	Hela-S3	cervix
19	chr13:52930000-52931200	Enhancers	HSMM	muscle
20	chr13:52930000-52931400	Enhancers	NHEK	skin

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