Variant report

Variant	rs2000670
Chromosome Location	chr18:29738782-29738783
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	chr18:29737699..29739046-chr18:30132133..30133008,6	MCF-7	breast:
2	chr18:29737678..29740541-chr18:29744932..29747295,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10502582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11081750	0.91[EUR][1000 genomes]
rs11081751	0.89[EUR][1000 genomes]
rs11661056	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12454857	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12457134	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12457138	0.90[EUR][1000 genomes]
rs12959368	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12962060	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1469168	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17735506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17804730	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2000671	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799636	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4799637	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62095576	0.82[EUR][1000 genomes]
rs62095577	0.80[EUR][1000 genomes]
rs62095578	0.89[EUR][1000 genomes]
rs62095579	0.90[EUR][1000 genomes]
rs62095587	0.90[EUR][1000 genomes]
rs62095588	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67929870	0.88[EUR][1000 genomes]
rs68120106	0.90[EUR][1000 genomes]
rs7232533	0.89[EUR][1000 genomes]
rs7234231	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7240197	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72639475	0.90[EUR][1000 genomes]
rs72942705	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9944759	0.90[EUR][1000 genomes]
rs9944778	0.90[EUR][1000 genomes]
rs9952622	0.90[EUR][1000 genomes]
rs9955753	0.91[EUR][1000 genomes]
rs9964960	0.90[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2000670	RNF138	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29738000-29739000	Active TSS	Duodenum Mucosa	Duodenum
2	chr18:29738400-29738800	Active TSS	Primary T cells from cord blood	blood
3	chr18:29738600-29738800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr18:29738600-29738800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr18:29738600-29738800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr18:29738600-29738800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr18:29738600-29738800	Flanking Active TSS	Colonic Mucosa	Colon
8	chr18:29738600-29738800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr18:29738600-29740200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr18:29738600-29740400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr18:29738600-29740400	Weak transcription	HMEC	breast
12	chr18:29738600-29741200	Enhancers	Fetal Intestine Large	intestine
13	chr18:29738600-29741200	Enhancers	Fetal Intestine Small	intestine
14	chr18:29738600-29741200	Enhancers	Rectal Mucosa Donor 31	rectum

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