Variant report

Variant	rs1578266
Chromosome Location	chr10:16233235-16233236
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10159534	0.84[AMR][1000 genomes]
rs10737010	0.94[EUR][1000 genomes]
rs10737011	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10752046	0.83[TSI][hapmap]
rs10795356	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10904693	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1340133	0.84[AMR][1000 genomes]
rs1340134	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1340137	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1340138	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1340139	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1417093	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1538762	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1577073	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591933	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1591934	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1832657	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856726	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1890848	0.86[ASN][1000 genomes]
rs2151948	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2185386	0.81[AMR][1000 genomes]
rs2486896	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2486906	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883626	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2991895	0.87[EUR][1000 genomes]
rs4575155	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4747265	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6602081	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6602082	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6602088	0.87[AMR][1000 genomes]
rs7081816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530146	chr10:15722937-16522747	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	esv3342684	chr10:16224995-16255206	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
3	nsv870420	chr10:16225427-16541252	Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv894904	chr10:16233175-16477106	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1578266	STAM	cis	cerebellum	SCAN
rs1578266	NMT2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:16217400-16239000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:16229000-16234400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr10:16229000-16235400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr10:16229000-16236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:16229200-16234400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr10:16229200-16234800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr10:16229200-16235000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr10:16232200-16234200	Weak transcription	Stomach Mucosa	stomach
9	chr10:16233200-16233400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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