Variant report

Variant	rs168503
Chromosome Location	chr2:54933177-54933178
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54926893..54929432-chr2:54932340..54933901,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10165490	0.84[CEU][hapmap]
rs10191922	0.86[ASN][1000 genomes]
rs11898012	0.83[CEU][hapmap]
rs168506	0.85[ASN][1000 genomes]
rs168507	0.85[EUR][1000 genomes]
rs168508	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs171350	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17416806	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs181348	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1821138	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs187124	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs191628	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2567835	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2931463	0.87[ASN][1000 genomes]
rs2941591	0.86[ASN][1000 genomes]
rs2971875	0.85[EUR][1000 genomes]
rs2971889	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs354187	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs354195	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs354209	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs354213	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs354214	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs354223	0.83[ASN][1000 genomes]
rs354224	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs354226	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs354228	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs354231	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs354236	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs354237	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs354238	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs354243	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671960	0.95[CEU][hapmap]
rs4671961	0.96[CEU][hapmap]

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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs168503	EML6	cis	Artery Tibial	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54922400-54935800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:54931200-54935200	Enhancers	HepG2	liver
3	chr2:54931800-54934800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:54931800-54935600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:54931800-54935800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:54931800-54935800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:54931800-54935800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:54931800-54935800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:54932000-54935800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:54932400-54935600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links