Variant report

Variant	rs7990079
Chromosome Location	chr13:40045976-40045977
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1014636	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1475175	0.84[CEU][hapmap]
rs1475176	0.84[CEU][hapmap]
rs1927196	0.84[CEU][hapmap]
rs2018	0.84[CEU][hapmap]
rs2148934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4499118	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4569130	0.80[MEX][hapmap];0.82[TSI][hapmap]
rs4943671	0.80[CEU][hapmap]
rs6563704	0.92[AFR][1000 genomes]
rs6563706	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs6563712	0.82[CEU][hapmap]
rs7322026	0.84[CEU][hapmap]
rs7324077	0.88[CEU][hapmap]
rs737645	0.80[MEX][hapmap];0.82[TSI][hapmap]
rs7489811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7981363	0.84[CEU][hapmap]
rs7982627	0.84[CEU][hapmap]
rs7996782	0.80[MEX][hapmap];0.82[TSI][hapmap]
rs8002691	0.84[CEU][hapmap]
rs912044	0.84[CEU][hapmap]
rs9315688	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315691	0.84[CEU][hapmap]
rs9315692	0.84[CEU][hapmap]
rs943568	0.88[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs9548785	0.84[CEU][hapmap]
rs9576808	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576811	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576812	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576824	0.84[CEU][hapmap]
rs9594334	0.84[CEU][hapmap]
rs9594335	0.84[CEU][hapmap]
rs9594336	0.83[CEU][hapmap]
rs9603543	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9603550	0.84[CEU][hapmap]
rs9741649	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	esv2757529	chr13:40040036-40090742	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2759933	chr13:40040036-40090742	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7990079	KIAA0564	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40037000-40051200	Weak transcription	Ovary	ovary
2	chr13:40037000-40053800	Weak transcription	Fetal Lung	lung
3	chr13:40037400-40053400	Weak transcription	Aorta	Aorta
4	chr13:40041600-40057800	Weak transcription	NHDF-Ad	bronchial
5	chr13:40042800-40047600	Weak transcription	Fetal Heart	heart
6	chr13:40043000-40048000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:40043600-40047800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:40043600-40068200	Weak transcription	Lung	lung
9	chr13:40043800-40047000	Weak transcription	Left Ventricle	heart
10	chr13:40044200-40048800	Weak transcription	Right Ventricle	heart
11	chr13:40045000-40046600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:40045400-40046000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:40045600-40046200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:40045600-40048800	Weak transcription	Right Atrium	heart

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