Variant report

Variant	rs12970341
Chromosome Location	chr18:24500399-24500400
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12455253	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12458362	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12956514	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12962943	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964548	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12965283	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12968314	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16942942	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16943002	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16943003	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16943019	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16943023	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16943028	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16943030	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16943033	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16943045	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16943049	0.91[CHB][hapmap];0.80[CHD][hapmap]
rs2020157	0.83[ASN][1000 genomes]
rs35269358	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35871650	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3865412	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3893013	0.91[CHB][hapmap]
rs4800273	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4800775	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4800776	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4800777	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71353412	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71353414	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71353415	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71353416	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71353417	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71370779	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9946779	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9948561	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9950360	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9957444	0.89[AMR][1000 genomes];0.84[EUR][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	esv2761995	chr18:24214286-24502570	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12970341	C18orf16	cis	brain	BrainEAC
rs12970341	C18orf16	cis	intralobular white matter	BrainEAC
rs12970341	C18orf16	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:24488400-24501200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:24499600-24500400	Enhancers	Fetal Muscle Leg	muscle
3	chr18:24499600-24501600	Enhancers	Liver	Liver
4	chr18:24499800-24500400	Enhancers	Fetal Intestine Small	intestine
5	chr18:24499800-24501400	Enhancers	HepG2	liver
6	chr18:24500000-24500400	Enhancers	Fetal Heart	heart
7	chr18:24500000-24501000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr18:24500000-24503800	Weak transcription	Gastric	stomach
9	chr18:24500000-24506600	Weak transcription	Brain Substantia Nigra	brain
10	chr18:24500200-24504800	Weak transcription	Ovary	ovary

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