Variant report

Variant	rs992592
Chromosome Location	chr5:98067832-98067833
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	chr5:98065365..98067941-chr5:98071458..98074162,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1002859	0.84[CHB][hapmap]
rs1508792	0.82[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1508793	0.82[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1818348	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1828169	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1911904	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1979980	0.82[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2249797	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2250807	0.84[CHB][hapmap]
rs2545671	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2545672	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2545675	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2545676	0.84[CHB][hapmap]
rs2545690	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2545730	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2545731	0.83[EUR][1000 genomes]
rs2545732	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2547965	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2547967	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2547970	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2547972	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2662258	0.81[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs2662264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2662267	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2662268	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2662271	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs331550	0.85[CHB][hapmap]
rs331551	0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs331552	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032060	chr5:98022226-98093492	Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv537817	chr5:98022226-98093492	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs992592	RGMB-AS1	cis	Muscle Skeletal	GTEx
rs992592	RGMB	cis	multi-tissue	Pritchard
rs992592	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs992592	RGMB	cis	normal skin	skin_eQTL
rs992592	RGMB	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98067800-98068000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links