Variant report

Variant	rs1923497
Chromosome Location	chr1:152423423-152423424
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152413761..152416710-chr1:152419995..152423681,3	MCF-7	breast:
2	chr1:152081901..152084932-chr1:152421607..152423575,3	MCF-7	breast:
3	chr1:152370172..152370928-chr1:152423235..152423954,2	MCF-7	breast:
4	chr1:152162027..152162959-chr1:152423046..152424098,5	MCF-7	breast:
5	chr1:152413939..152415718-chr1:152422401..152425266,2	K562	blood:
6	chr1:152369874..152370523-chr1:152423403..152423977,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10888487	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11205007	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11579061	0.83[AMR][1000 genomes]
rs1923492	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs1923500	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1951523	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2146114	1.00[ASW][hapmap];0.94[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2146115	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146118	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2203891	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240876	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4240877	0.94[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs4240878	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240879	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4240881	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs476589	0.86[ASN][1000 genomes]
rs4845432	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845434	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845763	0.94[CEU][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs561260	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587669	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6679896	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs941933	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv872443	chr1:152400055-152459747	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv872444	chr1:152400361-152440753	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv824664	chr1:152409024-152434443	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv463850	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv547858	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv872445	chr1:152411813-152440753	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1923497	SPRR2E	cis	parietal	SCAN
rs1923497	LYSMD1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152416400-152423800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:152422600-152423800	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links