Variant report

Variant	rs12959368
Chromosome Location	chr18:29739647-29739648
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	chr18:29737678..29740541-chr18:29744932..29747295,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10502582	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11081750	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11081751	0.86[EUR][1000 genomes]
rs11661056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12454857	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12457134	0.87[EUR][1000 genomes]
rs12457138	0.87[EUR][1000 genomes]
rs12962060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1469168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17735506	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17804730	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2000670	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2000671	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4799636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62095576	0.80[EUR][1000 genomes]
rs62095578	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62095579	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62095587	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62095588	0.88[EUR][1000 genomes]
rs67929870	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs68120106	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7232533	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7234231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7240197	0.88[EUR][1000 genomes]
rs72639475	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72942705	0.87[EUR][1000 genomes]
rs9944759	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9944778	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9952622	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9955753	0.88[EUR][1000 genomes]
rs9964960	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12959368	RNF138	Cis_1M	lymphoblastoid	RTeQTL
rs12959368	RNF138	cis	Thyroid	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29738600-29740200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr18:29738600-29740400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr18:29738600-29740400	Weak transcription	HMEC	breast
4	chr18:29738600-29741200	Enhancers	Fetal Intestine Large	intestine
5	chr18:29738600-29741200	Enhancers	Fetal Intestine Small	intestine
6	chr18:29738600-29741200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr18:29738800-29741200	Weak transcription	Colonic Mucosa	Colon
8	chr18:29739200-29740400	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links