Variant report

Variant	rs453658
Chromosome Location	chr6:29519848-29519849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:29519666-29521148	SK-N-SH	brain:	n/a	n/a
2	RFX5	chr6:29519835-29521028	K562	blood:	n/a	n/a
3	RFX5	chr6:29519591-29522025	IMR90	lung:	n/a	n/a
4	RFX5	chr6:29519768-29521722	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
OR2I1P	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1073339	0.82[EUR][1000 genomes]
rs1073340	0.82[EUR][1000 genomes]
rs11724	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233418	0.89[EUR][1000 genomes]
rs1233421	0.91[EUR][1000 genomes]
rs1233422	0.91[EUR][1000 genomes]
rs1233423	0.90[EUR][1000 genomes]
rs1233425	0.83[EUR][1000 genomes]
rs1233426	0.91[EUR][1000 genomes]
rs1233427	0.91[EUR][1000 genomes]
rs1592409	0.86[EUR][1000 genomes]
rs2223611	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2523425	0.90[EUR][1000 genomes]
rs2523427	0.82[EUR][1000 genomes]
rs2745402	0.86[EUR][1000 genomes]
rs2745403	0.90[EUR][1000 genomes]
rs2745406	0.83[EUR][1000 genomes]
rs2745408	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2745409	0.91[EUR][1000 genomes]
rs2745411	0.85[EUR][1000 genomes]
rs362513	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs362514	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs362540	0.85[EUR][1000 genomes]
rs362544	0.83[EUR][1000 genomes]
rs362546	0.91[EUR][1000 genomes]
rs370731	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs378956	0.92[EUR][1000 genomes]
rs394075	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs399166	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414282	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs414390	0.89[EUR][1000 genomes]
rs417374	0.92[EUR][1000 genomes]
rs419957	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs422241	0.89[EUR][1000 genomes]
rs422302	0.85[EUR][1000 genomes]
rs444013	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446198	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs909967	0.83[EUR][1000 genomes]
rs909968	0.91[EUR][1000 genomes]
rs969931	0.82[EUR][1000 genomes]
rs9968	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs453658	BTN1A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29515200-29521000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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