Variant report

Variant	rs1559854
Chromosome Location	chr11:84064300-84064301
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10792755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10792756	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs10898226	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10898227	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10898232	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11822426	0.85[YRI][hapmap]
rs3906479	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs3914464	0.92[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4310638	0.95[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs4547118	0.88[ASN][1000 genomes]
rs4636699	0.86[EUR][1000 genomes]
rs489716	0.92[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs4943892	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4943893	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs567263	0.92[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap]
rs568789	0.92[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs61897669	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6592176	0.95[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs6592177	0.92[ASW][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6592179	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs672796	0.92[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs7108323	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7117729	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[ASN][1000 genomes]
rs7118287	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7121832	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7124614	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7128063	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7128524	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7928824	0.89[AMR][1000 genomes]
rs7942296	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs7947614	0.92[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1559854	RBFA	trans	brain	seeQTL
rs1559854	TMEM126B	cis	parietal	SCAN

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

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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