Variant report

Variant	rs28847113
Chromosome Location	chr19:42338535-42338536
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	chr19:42337138..42340110-chr19:42342013..42344959,2	MCF-7	breast:
2	chr19:42337957..42339654-chr19:42347181..42349123,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LYPD4-1	chr19:42337740-42340005	ENSG00000267839.1

Variant related genes	Relation type
ENSG00000183103	Chromatin interaction
ENSG00000142025	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10401370	0.86[EUR][1000 genomes]
rs10401528	0.86[EUR][1000 genomes]
rs10401928	0.89[EUR][1000 genomes]
rs10407206	0.86[EUR][1000 genomes]
rs10407619	0.90[EUR][1000 genomes]
rs10407797	0.86[EUR][1000 genomes]
rs10408367	0.89[EUR][1000 genomes]
rs10410918	0.89[EUR][1000 genomes]
rs10414823	0.90[EUR][1000 genomes]
rs10416824	0.90[EUR][1000 genomes]
rs10418100	0.85[EUR][1000 genomes]
rs10419111	0.91[EUR][1000 genomes]
rs10419827	0.85[EUR][1000 genomes]
rs10426243	0.85[EUR][1000 genomes]
rs10500284	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12972552	0.80[AMR][1000 genomes]
rs12979253	0.88[EUR][1000 genomes]
rs1811564	0.89[EUR][1000 genomes]
rs1870093	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2008798	0.90[EUR][1000 genomes]
rs2008808	0.85[EUR][1000 genomes]
rs2199829	0.89[EUR][1000 genomes]
rs2199830	0.90[EUR][1000 genomes]
rs28821622	0.89[EUR][1000 genomes]
rs28824227	0.90[EUR][1000 genomes]
rs34819714	0.84[EUR][1000 genomes]
rs3795022	0.89[EUR][1000 genomes]
rs4480913	0.89[EUR][1000 genomes]
rs62117403	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6508998	0.89[EUR][1000 genomes]
rs6508999	0.89[EUR][1000 genomes]
rs6509000	0.88[EUR][1000 genomes]
rs7251154	0.81[EUR][1000 genomes]
rs7251336	0.86[EUR][1000 genomes]
rs7251783	0.86[EUR][1000 genomes]
rs7251799	0.86[EUR][1000 genomes]
rs7251960	0.84[EUR][1000 genomes]
rs734107	0.90[EUR][1000 genomes]
rs734109	0.90[EUR][1000 genomes]
rs8099934	0.90[EUR][1000 genomes]
rs8100182	0.90[EUR][1000 genomes]
rs8106505	0.90[EUR][1000 genomes]
rs8110199	0.90[EUR][1000 genomes]
rs8113283	0.88[EUR][1000 genomes]
rs8113538	0.89[EUR][1000 genomes]
rs8113641	0.89[EUR][1000 genomes]
rs8113720	0.89[EUR][1000 genomes]
rs8113741	0.89[EUR][1000 genomes]
rs8113813	0.89[EUR][1000 genomes]
rs899662	0.89[EUR][1000 genomes]

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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv960847	chr19:42319253-42339596	Enhancers Bivalent Enhancer Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28847113	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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