Variant report

Variant	rs12535487
Chromosome Location	chr7:112593810-112593811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112430077..112432189-chr7:112593600..112595306,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf60-1	chr7:112593368-112593811	NONHSAT122803
2	lnc-C7orf60-1	chr7:112593368-112593811	NONHSAT122804
3	lnc-C7orf60-1	chr7:112593368-112593811	NONHSAT122805
4	lnc-C7orf60-1	chr7:112593368-112593811	NONHSAT122806

Variant related genes	Relation type
ENSG00000146802	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10237980	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10246678	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10261874	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10275208	0.82[CHB][hapmap]
rs1227171	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1227174	0.86[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs1227190	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1238698	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs12539085	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1530756	0.82[CHB][hapmap]
rs1547554	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17160078	0.82[CHB][hapmap]
rs1718944	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1718967	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1796492	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1796493	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1796516	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1992988	0.82[CHD][hapmap]
rs1996843	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2396573	0.80[EUR][1000 genomes]
rs2396574	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs2457	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs2687267	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2708296	1.00[JPT][hapmap]
rs35548417	0.91[EUR][1000 genomes]
rs3997335	0.83[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3997336	0.81[EUR][1000 genomes]
rs494324	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs548994	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs549688	0.86[CEU][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552304	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[ASN][1000 genomes]
rs564494	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6466421	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs660743	0.85[JPT][hapmap]
rs672911	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs685259	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6944843	0.82[CHB][hapmap]
rs6948575	0.86[TSI][hapmap]
rs6953522	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7777973	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7781871	0.82[CHB][hapmap]
rs7785774	0.82[ASN][1000 genomes]
rs7803405	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs7808616	0.82[CHB][hapmap]
rs821782	0.82[ASN][1000 genomes]
rs821783	0.84[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs821785	0.86[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs821787	0.86[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9969347	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3692941	chr7:112571420-112614215	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription 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	2 gene(s)	inside rSNPs	n/a
4	nsv1027981	chr7:112577657-112613212	Weak transcription Active TSS Enhancers Flanking Active TSS 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	2 gene(s)	inside rSNPs	n/a
5	nsv1020911	chr7:112581515-112615249	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12535487	CAV2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112593800-112594200	ZNF genes & repeats	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links