Variant report

Variant	rs11230183
Chromosome Location	chr11:59965725-59965726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10897011	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11230147	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs11230160	0.83[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap]
rs11230161	0.85[CEU][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap]
rs11230180	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11230184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11230187	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11230194	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11230201	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1125357	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs11600716	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs11601689	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11603507	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11605427	0.96[CEU][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11826180	0.82[EUR][1000 genomes]
rs12453	0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1426250	0.84[CEU][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1426253	0.81[EUR][1000 genomes]
rs17528859	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs17529983	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs17602572	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1820428	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1820430	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834549	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834550	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834551	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834557	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015475	0.84[CEU][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs2070970	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs2081545	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081547	0.81[EUR][1000 genomes]
rs2123314	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278867	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583471	0.84[CEU][hapmap];0.92[JPT][hapmap]
rs2583476	0.83[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap]
rs2847655	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs2847663	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs2847666	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs2847667	0.80[CEU][hapmap]
rs2847668	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs2855017	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs28628869	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28672915	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4492839	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4939311	0.85[CEU][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap]
rs4939312	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs4939320	0.82[EUR][1000 genomes]
rs516478	0.84[CEU][hapmap]
rs56189574	0.82[ASN][1000 genomes]
rs56201148	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56273223	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56357056	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs583791	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs606588	0.82[CEU][hapmap]
rs610932	0.85[CEU][hapmap]
rs611418	0.81[CEU][hapmap]
rs624663	0.84[CEU][hapmap]
rs631853	0.85[CEU][hapmap]
rs632185	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs636147	0.89[CEU][hapmap]
rs655231	0.81[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap]
rs662196	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs688030	0.80[CEU][hapmap]
rs7116190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72918674	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72920867	0.80[EUR][1000 genomes]
rs764859	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7926344	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926354	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926729	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926954	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7928895	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7929589	0.82[EUR][1000 genomes]
rs7933202	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7933805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935829	0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7936120	0.81[EUR][1000 genomes]
rs7939882	0.94[EUR][1000 genomes]
rs7946992	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920573	0.85[CEU][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]

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	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv832174	chr11:59909267-60073908	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11230183	FAM111A	cis	parietal	SCAN
rs11230183	LGALS12	cis	cerebellum	SCAN
rs11230183	MS4A4A	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59965000-59966200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr11:59965000-59969400	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr11:59965600-59969400	Weak transcription	Monocytes-CD14+_RO01746	blood

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