Variant report

Variant	rs17739527
Chromosome Location	chr1:112570739-112570740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:112567436..112574679-chr17:59473442..59479631,13	MCF-7	breast:
2	chr1:112538553..112540898-chr1:112568252..112571244,2	MCF-7	breast:
3	chr1:112546466..112549433-chr1:112570066..112572222,2	MCF-7	breast:
4	chr1:112565683..112570763-chr17:59483597..59489037,9	MCF-7	breast:
5	chr1:112569948..112575057-chr17:59473695..59479360,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121068	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000267131	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12724483	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12749667	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12751286	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372861	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443925	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171994	1.00[ASN][1000 genomes]
rs2819209	1.00[ASN][1000 genomes]
rs3008534	1.00[ASN][1000 genomes]
rs3017628	1.00[ASN][1000 genomes]
rs34751177	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367572	1.00[ASN][1000 genomes]
rs373157	1.00[ASN][1000 genomes]
rs374902	1.00[ASN][1000 genomes]
rs374958	1.00[ASN][1000 genomes]
rs400151	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4088223	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430680	1.00[ASN][1000 genomes]
rs432663	1.00[ASN][1000 genomes]
rs434800	1.00[ASN][1000 genomes]
rs436173	1.00[ASN][1000 genomes]
rs436818	1.00[ASN][1000 genomes]
rs441740	1.00[ASN][1000 genomes]
rs443625	1.00[ASN][1000 genomes]
rs450822	1.00[ASN][1000 genomes]
rs455228	1.00[ASN][1000 genomes]
rs460443	1.00[ASN][1000 genomes]
rs461311	1.00[ASN][1000 genomes]
rs461553	1.00[ASN][1000 genomes]
rs462936	1.00[ASN][1000 genomes]
rs463983	1.00[ASN][1000 genomes]
rs464357	1.00[ASN][1000 genomes]
rs464819	1.00[ASN][1000 genomes]
rs466206	1.00[ASN][1000 genomes]
rs4838935	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609882	1.00[ASN][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	nsv831048	chr1:112459697-112680279	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv831059	chr1:112569062-112724725	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17739527	SLC16A1	cis	parietal	SCAN
rs17739527	GSTM3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112568800-112574200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:112569200-112572000	Enhancers	Brain Germinal Matrix	brain
3	chr1:112569600-112578000	Enhancers	Fetal Stomach	stomach
4	chr1:112569800-112571000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:112570400-112570800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:112570600-112570800	Enhancers	Pancreas	Pancrea

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