Variant report

Variant	rs9989546
Chromosome Location	chr18:12562537-12562538
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12561120..12563206-chr18:12574921..12576824,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10048276	0.87[ASN][1000 genomes]
rs1105122	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11660232	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11662531	0.87[ASN][1000 genomes]
rs11663289	0.84[EUR][1000 genomes]
rs11663358	1.00[ASN][1000 genomes]
rs11663668	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11664013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11664068	0.87[ASN][1000 genomes]
rs11664219	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11664431	0.81[EUR][1000 genomes]
rs11664773	1.00[ASN][1000 genomes]
rs11665415	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11665542	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1592641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17595746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1940973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155699	1.00[ASN][1000 genomes]
rs2186906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28527375	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28565322	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28575715	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634564	0.87[ASN][1000 genomes]
rs28663159	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28801690	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28815517	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28821540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4797689	1.00[ASW][hapmap]
rs56029848	1.00[ASN][1000 genomes]
rs56870830	1.00[ASN][1000 genomes]
rs57706356	1.00[ASN][1000 genomes]
rs58638386	1.00[ASN][1000 genomes]
rs60563648	1.00[ASN][1000 genomes]
rs61027502	0.87[ASN][1000 genomes]
rs73405602	1.00[ASN][1000 genomes]
rs73407510	1.00[ASN][1000 genomes]
rs73407511	1.00[ASN][1000 genomes]
rs73407524	1.00[ASN][1000 genomes]
rs9946557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9953831	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9959145	0.83[CEU][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959201	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9960604	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9960706	0.87[ASN][1000 genomes]
rs9963755	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9966118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9989546	SLMO1	cis	cerebellum	SCAN
rs9989546	RNMT	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12553600-12567600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr18:12553600-12574600	Weak transcription	Right Ventricle	heart
3	chr18:12553800-12569600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr18:12554200-12567600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr18:12557600-12580800	Weak transcription	Pancreas	Pancrea
6	chr18:12558400-12569000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr18:12558400-12569200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr18:12558600-12570200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr18:12559600-12564200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr18:12559600-12569200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:12559800-12574600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:12560600-12569200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links