Variant report

Variant	rs17085643
Chromosome Location	chr13:70487282-70487283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BORA-23	chr13:70487274-70487381	NONHSAT034249

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11617171	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11618596	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17085438	1.00[CHD][hapmap]
rs17085443	1.00[CHD][hapmap]
rs17085444	1.00[CHD][hapmap]
rs17085605	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2113357	1.00[CHD][hapmap]
rs2911504	1.00[CHD][hapmap]
rs2911506	1.00[CHD][hapmap]
rs2911518	1.00[CHD][hapmap]
rs2911519	1.00[CHD][hapmap]
rs2911522	1.00[CHB][hapmap]
rs3012107	1.00[CHD][hapmap]
rs3012108	1.00[CHD][hapmap]
rs56156636	0.87[ASN][1000 genomes]
rs59614129	0.87[ASN][1000 genomes]
rs7332190	1.00[JPT][hapmap]
rs7334775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7337519	1.00[CHD][hapmap]
rs74090650	0.87[ASN][1000 genomes]
rs74090659	0.87[ASN][1000 genomes]
rs7986882	0.87[ASN][1000 genomes]
rs9529627	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900481	chr13:70147851-70560731	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1054554	chr13:70159715-70502956	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv900487	chr13:70327693-70548643	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv530724	chr13:70393680-71164323	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1045918	chr13:70409675-70615997	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1038695	chr13:70484098-70654204	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv900488	chr13:70487282-70560731	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv900489	chr13:70487282-70578306	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17085643	CAV2	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:70486600-70495000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:70487000-70487600	Enhancers	Fetal Muscle Leg	muscle

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