Variant report

Variant	rs12223480
Chromosome Location	chr11:101616696-101616697
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1006330	0.92[ASN][1000 genomes]
rs10458947	0.83[AMR][1000 genomes]
rs10459002	0.88[ASN][1000 genomes]
rs10459003	0.83[AMR][1000 genomes]
rs10466637	0.82[AMR][1000 genomes]
rs10750618	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750619	0.86[AMR][1000 genomes]
rs10791521	0.89[AMR][1000 genomes]
rs10791522	0.86[AMR][1000 genomes]
rs10791525	0.80[AMR][1000 genomes]
rs10791526	0.86[AMR][1000 genomes]
rs10895191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10895193	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895196	0.87[AMR][1000 genomes]
rs10895197	0.87[AMR][1000 genomes]
rs10895198	0.85[AMR][1000 genomes]
rs10895200	0.85[AMR][1000 genomes]
rs11224994	0.92[ASN][1000 genomes]
rs11224995	0.88[ASN][1000 genomes]
rs11225004	0.82[ASN][1000 genomes]
rs11225005	0.82[ASN][1000 genomes]
rs11225009	0.80[AMR][1000 genomes]
rs11225011	0.81[ASN][1000 genomes]
rs11225012	0.81[ASN][1000 genomes]
rs11225015	0.80[ASN][1000 genomes]
rs11599998	0.80[AMR][1000 genomes]
rs12361399	0.91[ASN][1000 genomes]
rs12361929	0.91[ASN][1000 genomes]
rs17746310	0.91[ASN][1000 genomes]
rs1939025	0.87[AMR][1000 genomes]
rs1939043	0.90[ASN][1000 genomes]
rs1939046	0.91[ASN][1000 genomes]
rs1939053	0.82[ASN][1000 genomes]
rs1939055	0.80[ASN][1000 genomes]
rs1939057	0.81[AMR][1000 genomes]
rs1939059	0.85[AMR][1000 genomes]
rs1939064	0.92[ASN][1000 genomes]
rs1939066	0.80[AMR][1000 genomes]
rs1939071	0.90[AMR][1000 genomes]
rs1939072	0.91[ASN][1000 genomes]
rs1939073	0.89[AMR][1000 genomes]
rs1939437	0.90[AMR][1000 genomes]
rs1939458	1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs1939460	0.91[ASN][1000 genomes]
rs1954765	0.87[ASN][1000 genomes]
rs2105613	0.90[ASN][1000 genomes]
rs2155057	0.89[AMR][1000 genomes]
rs2155058	0.89[AMR][1000 genomes]
rs2155060	0.90[ASN][1000 genomes]
rs2155061	0.90[AMR][1000 genomes]
rs2155062	0.90[ASN][1000 genomes]
rs2155063	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2186609	0.90[ASN][1000 genomes]
rs2186610	0.90[AMR][1000 genomes]
rs4414186	0.80[ASN][1000 genomes]
rs4429028	0.82[ASN][1000 genomes]
rs4548585	0.80[ASN][1000 genomes]
rs4586114	0.87[ASN][1000 genomes]
rs4754790	0.91[ASN][1000 genomes]
rs4754791	0.91[ASN][1000 genomes]
rs4754792	0.89[ASN][1000 genomes]
rs4754798	0.88[ASN][1000 genomes]
rs4754801	0.81[ASN][1000 genomes]
rs4754803	0.80[ASN][1000 genomes]
rs4754804	0.80[ASN][1000 genomes]
rs55854918	0.81[ASN][1000 genomes]
rs56245539	0.90[ASN][1000 genomes]
rs61916463	0.89[ASN][1000 genomes]
rs6590918	0.89[AMR][1000 genomes]
rs7104516	0.80[AMR][1000 genomes]
rs7105933	0.90[ASN][1000 genomes]
rs7131271	0.80[AMR][1000 genomes]
rs72986459	0.84[ASN][1000 genomes]
rs732086	0.90[AMR][1000 genomes]
rs7924364	0.81[AMR][1000 genomes]
rs7929894	0.90[ASN][1000 genomes]
rs7931237	0.87[ASN][1000 genomes]
rs7949648	0.86[ASN][1000 genomes]
rs9988826	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898330	chr11:101243644-101722031	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1052159	chr11:101439655-101853293	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1051457	chr11:101446705-101837650	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv530645	chr11:101451416-101778666	Bivalent/Poised TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv468853	chr11:101539408-101616696	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv556139	chr11:101539408-101616696	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv898332	chr11:101562004-101732566	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv832249	chr11:101571819-101749073	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1044223	chr11:101586478-101626839	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12223480	MMP13	cis	cerebellum	SCAN
rs12223480	BIRC2	cis	parietal	SCAN
rs12223480	CD300C	trans	parietal	SCAN
rs12223480	PIGO	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101613200-101619400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:101616200-101616800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:101616200-101617000	Enhancers	Fetal Lung	lung

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