Variant report

Variant	rs12953982
Chromosome Location	chr18:24600534-24600535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10502482	0.96[ASN][1000 genomes]
rs12954200	0.85[ASN][1000 genomes]
rs12963112	0.83[ASN][1000 genomes]
rs12965711	0.84[ASN][1000 genomes]
rs12966203	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12966301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12967710	0.83[ASN][1000 genomes]
rs12968314	0.90[AFR][1000 genomes]
rs1436902	0.99[ASN][1000 genomes]
rs1436906	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943033	0.92[AFR][1000 genomes]
rs16943045	0.84[ASW][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap]
rs16943049	0.90[JPT][hapmap]
rs16943089	0.89[ASN][1000 genomes]
rs16943144	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16943156	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16943160	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16943161	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16943164	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16943175	0.97[ASN][1000 genomes]
rs16943178	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16943184	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960687	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1821789	0.89[ASN][1000 genomes]
rs1941113	0.96[ASN][1000 genomes]
rs28564652	0.89[ASN][1000 genomes]
rs28647464	0.84[ASN][1000 genomes]
rs34738073	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35269358	0.90[AFR][1000 genomes]
rs35443853	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35507377	0.87[ASN][1000 genomes]
rs35725335	0.83[ASN][1000 genomes]
rs3893013	0.90[JPT][hapmap]
rs4800274	0.88[ASN][1000 genomes]
rs4800777	0.83[AFR][1000 genomes]
rs4800782	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56218423	0.89[ASN][1000 genomes]
rs60742277	0.89[ASN][1000 genomes]
rs60856601	0.89[ASN][1000 genomes]
rs6508462	0.89[ASN][1000 genomes]
rs71353424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717284	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7229046	0.89[ASN][1000 genomes]
rs7234761	0.96[ASN][1000 genomes]
rs7236637	0.89[ASN][1000 genomes]
rs8087494	0.89[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	nsv833600	chr18:24473894-24681019	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv909472	chr18:24479960-24614192	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1067103	chr18:24524011-24760469	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv543668	chr18:24524011-24760469	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12953982	C18orf16	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:24591000-24601200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:24596400-24600800	Weak transcription	Pancreas	Pancrea
3	chr18:24598800-24601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr18:24599000-24602600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr18:24599200-24600800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr18:24599400-24604800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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