Variant report

Variant	rs60835840
Chromosome Location	chr12:123860939-123860940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123859632..123861218-chr12:123970833..123973407,2	K562	blood:
2	chr12:123849812..123851534-chr12:123858422..123861381,2	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10082867	0.97[ASN][1000 genomes]
rs10444439	0.85[ASN][1000 genomes]
rs10444449	0.82[ASN][1000 genomes]
rs10773003	0.93[ASN][1000 genomes]
rs10773004	0.95[ASN][1000 genomes]
rs10773005	0.95[ASN][1000 genomes]
rs10773006	0.95[ASN][1000 genomes]
rs10846497	0.81[ASN][1000 genomes]
rs10846505	0.88[ASN][1000 genomes]
rs10846506	0.93[ASN][1000 genomes]
rs11057238	0.83[ASN][1000 genomes]
rs11057242	0.91[ASN][1000 genomes]
rs11057248	0.92[ASN][1000 genomes]
rs11057251	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11057254	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057261	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057273	0.97[ASN][1000 genomes]
rs11057275	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057276	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057284	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11503021	0.93[ASN][1000 genomes]
rs11608297	0.85[ASN][1000 genomes]
rs11608305	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11611141	0.97[ASN][1000 genomes]
rs11611677	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11611679	0.92[ASN][1000 genomes]
rs11611680	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11611694	0.97[ASN][1000 genomes]
rs12317103	0.97[ASN][1000 genomes]
rs12317452	0.95[ASN][1000 genomes]
rs12366872	0.97[ASN][1000 genomes]
rs12367421	0.93[ASN][1000 genomes]
rs12582153	0.93[ASN][1000 genomes]
rs13303208	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28410096	0.98[ASN][1000 genomes]
rs28414347	0.81[ASN][1000 genomes]
rs28417583	0.81[ASN][1000 genomes]
rs28419092	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28450974	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28461471	0.98[ASN][1000 genomes]
rs28496545	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28498205	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28501453	0.81[ASN][1000 genomes]
rs28503862	0.98[ASN][1000 genomes]
rs28516750	0.94[ASN][1000 genomes]
rs28532037	0.98[ASN][1000 genomes]
rs28533432	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28537583	0.81[ASN][1000 genomes]
rs28546238	0.81[ASN][1000 genomes]
rs28556815	0.88[ASN][1000 genomes]
rs28565984	0.85[ASN][1000 genomes]
rs28574664	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28577594	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28581850	0.98[ASN][1000 genomes]
rs28587386	0.81[ASN][1000 genomes]
rs28592032	0.98[ASN][1000 genomes]
rs28595660	0.81[ASN][1000 genomes]
rs28602967	0.81[ASN][1000 genomes]
rs28611282	0.81[ASN][1000 genomes]
rs28613486	0.81[ASN][1000 genomes]
rs28631104	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28642812	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28681105	0.81[ASN][1000 genomes]
rs28690326	0.86[ASN][1000 genomes]
rs28786830	0.98[ASN][1000 genomes]
rs28820735	0.98[ASN][1000 genomes]
rs28825193	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28865692	0.81[ASN][1000 genomes]
rs28866344	0.94[ASN][1000 genomes]
rs28885203	0.81[ASN][1000 genomes]
rs3088303	0.93[ASN][1000 genomes]
rs34032470	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35818434	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4759375	0.95[ASN][1000 genomes]
rs4759377	0.97[ASN][1000 genomes]
rs56116847	0.96[ASN][1000 genomes]
rs56197170	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56309603	0.90[ASN][1000 genomes]
rs61388686	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61955125	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6416290	0.84[ASN][1000 genomes]
rs6488873	0.88[ASN][1000 genomes]
rs7298909	0.97[ASN][1000 genomes]
rs7303754	0.80[ASN][1000 genomes]
rs7312145	0.97[ASN][1000 genomes]
rs7315453	0.97[ASN][1000 genomes]
rs73216931	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73231950	0.93[ASN][1000 genomes]
rs7954704	0.97[ASN][1000 genomes]
rs7972811	0.97[ASN][1000 genomes]
rs7974099	0.87[ASN][1000 genomes]
rs9669273	0.97[ASN][1000 genomes]
rs9669295	0.96[ASN][1000 genomes]
rs9705407	0.93[ASN][1000 genomes]
rs9739171	0.97[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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv826534	chr12:123859610-123876354	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs60835840	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs60835840	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs60835840	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs60835840	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs60835840	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs60835840	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs60835840	LOC283378	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123850600-123867200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:123850600-123867800	Weak transcription	Right Atrium	heart
3	chr12:123859200-123867200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:123859600-123863400	Weak transcription	A549	lung
5	chr12:123859600-123863400	Weak transcription	HepG2	liver
6	chr12:123860000-123861000	Weak transcription	K562	blood
7	chr12:123860000-123863200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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