Variant report

Variant	rs2533045
Chromosome Location	chr14:72320905-72320906
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:72319702..72321484-chr14:72327900..72329836,2	MCF-7	breast:
2	chr14:72314229..72318890-chr14:72319811..72323615,5	MCF-7	breast:
3	chr14:72218474..72220315-chr14:72319928..72323369,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266869	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10132551	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10134940	1.00[EUR][1000 genomes]
rs10139169	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10145833	1.00[EUR][1000 genomes]
rs10148887	1.00[EUR][1000 genomes]
rs2533041	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533042	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2533043	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533046	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2533047	0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2533048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533049	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2533050	0.91[ASN][1000 genomes]
rs2533052	0.92[ASN][1000 genomes]
rs2533054	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2533060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28706853	1.00[EUR][1000 genomes]
rs6574022	1.00[EUR][1000 genomes]
rs7141201	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7151501	0.90[EUR][1000 genomes]
rs8022087	0.90[EUR][1000 genomes]
rs887404	0.92[ASN][1000 genomes]
rs887405	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv565044	chr14:72317961-72336142	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2533045	SLC5A7	trans	brain	seeQTL
rs2533045	LRTM1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72316600-72322600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:72319600-72322800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:72319600-72322800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:72319600-72323000	Weak transcription	Fetal Heart	heart
5	chr14:72320800-72321000	Enhancers	Left Ventricle	heart
6	chr14:72320800-72321000	Enhancers	Spleen	Spleen

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