Variant report

Variant	rs4756988
Chromosome Location	chr11:19110777-19110778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1012929	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1039512	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10833057	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10833058	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10833059	0.86[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10833060	0.98[EUR][1000 genomes]
rs10833061	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10833062	0.82[CEU][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs11024984	0.94[ASN][1000 genomes]
rs11024997	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11025001	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11025009	0.91[ASN][1000 genomes]
rs11025010	0.91[ASN][1000 genomes]
rs11025011	0.97[EUR][1000 genomes]
rs11025013	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11025014	0.81[AMR][1000 genomes]
rs11025018	0.85[MEX][hapmap];0.81[TSI][hapmap]
rs11601935	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11606080	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11606222	0.81[AMR][1000 genomes]
rs11608243	0.81[TSI][hapmap]
rs12223284	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs16936167	0.81[TSI][hapmap]
rs1962511	0.93[ASN][1000 genomes]
rs2089051	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4756987	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756989	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4757751	0.99[ASN][1000 genomes]
rs4757753	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7123033	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs7125292	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7125667	0.99[ASN][1000 genomes]
rs7125678	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs962317	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040805	chr11:19037871-19892803	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv540957	chr11:19037871-19892803	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4756988	NAV2	cis	cerebellum	SCAN
rs4756988	ZDHHC13	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19104800-19111800	Weak transcription	Esophagus	oesophagus
2	chr11:19108200-19113400	Enhancers	HUVEC	blood vessel
3	chr11:19109800-19110800	Weak transcription	NHEK	skin
4	chr11:19109800-19111800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:19110000-19112000	Weak transcription	NH-A	brain
6	chr11:19110000-19115400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:19110400-19112800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:19110600-19112000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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