Variant report

Variant	rs56125264
Chromosome Location	chr2:99516699-99516700
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99514144..99517054-chr2:99525112..99527785,2	MCF-7	breast:
2	chr2:99224479..99226496-chr2:99514004..99516760,2	MCF-7	breast:
3	chr2:99514955..99516765-chr2:99517023..99518903,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115446	Chromatin interaction
ENSG00000183513	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10172158	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10192266	0.81[AMR][1000 genomes]
rs11123755	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12468024	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12474283	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12712038	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12712041	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712043	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13004700	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13005124	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13011428	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13025076	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13025913	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13028500	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1581251	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1607256	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1976766	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4311103	0.89[ASN][1000 genomes]
rs4850889	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4850890	0.89[ASN][1000 genomes]
rs4851167	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4851170	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4851171	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4851173	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851174	0.82[AMR][1000 genomes]
rs4851175	0.82[AMR][1000 genomes]
rs4851177	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6419564	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542843	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542845	0.89[ASN][1000 genomes]
rs6714243	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6717372	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6739176	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6739503	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6742047	0.82[AMR][1000 genomes]
rs7608889	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs925887	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56125264	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99500000-99517000	Weak transcription	Gastric	stomach
2	chr2:99511200-99520400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:99512000-99526000	Weak transcription	Right Atrium	heart
4	chr2:99513200-99525000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:99513400-99520600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:99515200-99524600	Weak transcription	Pancreas	Pancrea
7	chr2:99515800-99520600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:99516200-99517000	Weak transcription	Lung	lung

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