Variant report

Variant	rs12136090
Chromosome Location	chr1:184175041-184175042
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	chr1:184173763..184175918-chr1:184179774..184182386,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10494575	0.87[ASN][1000 genomes]
rs10494577	0.82[EUR][1000 genomes]
rs10911521	0.90[EUR][1000 genomes]
rs10911523	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911528	0.95[EUR][1000 genomes]
rs10911529	0.85[EUR][1000 genomes]
rs10911541	0.82[EUR][1000 genomes]
rs12119073	0.82[EUR][1000 genomes]
rs12119930	0.93[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.89[EUR][1000 genomes]
rs12119989	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs12129040	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132917	0.85[EUR][1000 genomes]
rs12142293	0.93[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap]
rs12401350	0.81[EUR][1000 genomes]
rs12401732	0.89[EUR][1000 genomes]
rs12402004	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12402028	0.89[EUR][1000 genomes]
rs12402670	0.82[EUR][1000 genomes]
rs12403264	0.89[EUR][1000 genomes]
rs12406379	0.87[ASN][1000 genomes]
rs12408100	0.85[EUR][1000 genomes]
rs12726078	0.82[EUR][1000 genomes]
rs12742417	0.81[EUR][1000 genomes]
rs12746749	0.82[EUR][1000 genomes]
rs12756256	0.84[EUR][1000 genomes]
rs1327142	0.93[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap]
rs1409808	0.84[EUR][1000 genomes]
rs1409810	0.85[EUR][1000 genomes]
rs1854085	0.85[EUR][1000 genomes]
rs2161989	0.85[EUR][1000 genomes]
rs2194700	0.94[EUR][1000 genomes]
rs2378818	0.89[EUR][1000 genomes]
rs2378820	0.89[EUR][1000 genomes]
rs2378840	0.82[EUR][1000 genomes]
rs34301155	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34306471	0.85[EUR][1000 genomes]
rs34518379	0.89[EUR][1000 genomes]
rs36086128	0.89[EUR][1000 genomes]
rs4651179	0.93[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap]
rs58294748	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6660720	0.89[EUR][1000 genomes]
rs6670049	0.85[EUR][1000 genomes]
rs6690614	0.82[EUR][1000 genomes]
rs6694958	0.89[EUR][1000 genomes]
rs6696567	0.87[EUR][1000 genomes]
rs6697294	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518664	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890065	0.82[EUR][1000 genomes]
rs929942	0.89[EUR][1000 genomes]
rs9650990	0.93[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.89[EUR][1000 genomes]
rs986595	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1006655	chr1:183922288-184186677	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12136090	C1orf125	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184162600-184191400	Weak transcription	Right Ventricle	heart
2	chr1:184169200-184187600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:184171600-184179000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:184171600-184179200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:184174800-184176400	Enhancers	Fetal Heart	heart
6	chr1:184175000-184175200	Enhancers	Left Ventricle	heart

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