Variant report

Variant	rs12892913
Chromosome Location	chr14:72633215-72633216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10483841	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11845670	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11845720	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[ASN][1000 genomes]
rs12590752	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12880584	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs12882756	0.91[CHB][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs12885156	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890911	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12891614	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12895540	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12896782	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238246	0.87[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2238247	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2238248	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2238249	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2238250	0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2238251	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2238252	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2238253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283410	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2283411	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2283412	0.87[CEU][hapmap];0.80[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2283413	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2283414	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2332802	1.00[ASW][hapmap];0.91[CHB][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34206394	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34233242	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35304669	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7161011	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.94[MEX][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7494363	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
3	esv3397769	chr14:72633051-72633222	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12892913	RDH12	cis	parietal	SCAN
rs12892913	COX16	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72620400-72633400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:72624200-72638600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr14:72626200-72645800	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links