Variant report

Variant	rs4493131
Chromosome Location	chr18:12588628-12588629
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12588552..12590477-chr18:12592485..12594002,2	MCF-7	breast:

Extended variants
information (count: 127 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10401097	0.82[ASN][1000 genomes]
rs10445428	0.88[ASN][1000 genomes]
rs11080582	0.88[ASN][1000 genomes]
rs11080583	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080584	0.90[ASN][1000 genomes]
rs11080585	0.83[ASN][1000 genomes]
rs11080586	0.84[ASN][1000 genomes]
rs11080590	0.81[ASN][1000 genomes]
rs11659854	0.83[ASN][1000 genomes]
rs11663958	0.83[ASN][1000 genomes]
rs11664765	0.82[ASN][1000 genomes]
rs11664861	0.85[ASN][1000 genomes]
rs11664914	0.85[ASN][1000 genomes]
rs11664917	0.85[ASN][1000 genomes]
rs11664936	0.83[ASN][1000 genomes]
rs11665543	0.83[ASN][1000 genomes]
rs12326271	0.82[ASN][1000 genomes]
rs12454931	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12455093	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12455909	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12457903	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12604184	0.82[ASN][1000 genomes]
rs12604385	0.89[ASN][1000 genomes]
rs12604400	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12604541	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12605240	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12605392	0.85[ASN][1000 genomes]
rs12606506	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12953406	0.88[ASN][1000 genomes]
rs12953578	0.82[ASN][1000 genomes]
rs12954614	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12955161	0.86[ASN][1000 genomes]
rs12955490	0.85[ASN][1000 genomes]
rs12956133	0.82[ASN][1000 genomes]
rs12956885	0.84[ASN][1000 genomes]
rs12957151	0.90[ASN][1000 genomes]
rs12957688	0.83[ASN][1000 genomes]
rs12958200	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12959015	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12960150	0.82[ASN][1000 genomes]
rs12961966	0.88[ASN][1000 genomes]
rs12962476	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12963179	0.83[ASN][1000 genomes]
rs12963325	0.84[ASN][1000 genomes]
rs12964660	0.86[ASN][1000 genomes]
rs12965094	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12970025	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12970174	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1893193	0.86[ASN][1000 genomes]
rs1940974	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1940975	0.83[ASN][1000 genomes]
rs2155698	0.83[ASN][1000 genomes]
rs2186907	0.84[ASN][1000 genomes]
rs28414067	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28457089	0.83[EUR][1000 genomes]
rs28496036	0.89[ASN][1000 genomes]
rs28582228	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28647784	0.83[EUR][1000 genomes]
rs28886423	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34072260	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34178879	0.88[ASN][1000 genomes]
rs34438212	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34456643	0.89[ASN][1000 genomes]
rs34814556	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34899007	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35449211	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35630805	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35963756	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4389196	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4627434	0.83[ASN][1000 genomes]
rs4629035	0.82[ASN][1000 genomes]
rs55749182	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58215411	0.88[ASN][1000 genomes]
rs60505421	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62097102	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62097103	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62097126	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62097148	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62097149	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62097152	0.80[ASN][1000 genomes]
rs62097153	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67045810	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67268432	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs70964152	0.83[ASN][1000 genomes]
rs7234697	0.83[ASN][1000 genomes]
rs7238546	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7242395	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7504857	0.80[ASN][1000 genomes]
rs755020	0.85[ASN][1000 genomes]
rs755021	0.85[ASN][1000 genomes]
rs8086094	0.85[ASN][1000 genomes]
rs8088786	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8089081	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8089619	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8093129	0.84[ASN][1000 genomes]
rs8093571	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8095160	0.83[ASN][1000 genomes]
rs8096455	0.82[ASN][1000 genomes]
rs9303772	0.82[ASN][1000 genomes]
rs9303773	0.82[ASN][1000 genomes]
rs948301	0.85[ASN][1000 genomes]
rs948302	0.85[ASN][1000 genomes]
rs948303	0.82[ASN][1000 genomes]
rs9675543	0.85[ASN][1000 genomes]
rs9710023	0.81[EUR][1000 genomes]
rs9945339	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9945374	0.82[EUR][1000 genomes]
rs9947738	0.84[ASN][1000 genomes]
rs9948505	0.82[ASN][1000 genomes]
rs9948618	0.80[ASN][1000 genomes]
rs9951147	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9954054	0.82[ASN][1000 genomes]
rs9958409	0.82[ASN][1000 genomes]
rs9959759	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9960824	0.80[ASN][1000 genomes]
rs9961705	0.86[EUR][1000 genomes]
rs9961851	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9964759	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9965123	0.82[ASN][1000 genomes]
rs9989496	0.81[ASN][1000 genomes]
rs9989506	0.82[ASN][1000 genomes]
rs9989568	0.82[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	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	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
4	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
5	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
rs4493131	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs4493131	SPIRE1	cis	Muscle Skeletal	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12570000-12595600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:12579400-12588800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr18:12587000-12589200	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr18:12587000-12592600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:12587400-12589200	Weak transcription	Fetal Brain Female	brain
6	chr18:12587800-12596800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr18:12588000-12595400	Weak transcription	Fetal Heart	heart
8	chr18:12588600-12588800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr18:12588600-12589800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr18:12588600-12589800	Enhancers	Brain Hippocampus Middle	brain
11	chr18:12588600-12589800	Enhancers	Brain Substantia Nigra	brain
12	chr18:12588600-12589800	Enhancers	HepG2	liver
13	chr18:12588600-12590800	Enhancers	Liver	Liver
14	chr18:12588600-12591400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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