Variant report

Variant	rs1559855
Chromosome Location	chr11:84064236-84064237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10128620	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10160220	0.90[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10501561	1.00[JPT][hapmap]
rs10792757	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10898221	1.00[JPT][hapmap]
rs10898229	1.00[JPT][hapmap]
rs10898230	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10898231	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10898233	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11233966	1.00[JPT][hapmap]
rs11233969	1.00[JPT][hapmap]
rs11234001	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12274848	1.00[JPT][hapmap]
rs12277167	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12282279	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12283368	1.00[JPT][hapmap]
rs12286690	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs12360734	1.00[JPT][hapmap]
rs1559856	0.93[CEU][hapmap];0.91[YRI][hapmap]
rs17147295	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7111688	1.00[JPT][hapmap]
rs7928075	0.94[ASW][hapmap];0.93[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9988803	1.00[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948410	chr11:83918339-84812001	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1038641	chr11:83996453-84334045	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv541103	chr11:83996453-84334045	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1049696	chr11:84039547-84116297	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv898031	chr11:84060342-84379671	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1559855	CCDC90B	cis	parietal	SCAN
rs1559855	TMEM126B	cis	parietal	SCAN
rs1559855	MXRA7	trans	lymphoblastoid	seeQTL

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

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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