Variant report

Variant	rs12223690
Chromosome Location	chr11:8901824-8901825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8892466..8895053-chr11:8899767..8902040,2	K562	blood:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10279	0.91[JPT][hapmap]
rs10840135	0.80[YRI][hapmap]
rs10840139	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11042105	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11042106	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11042107	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11042108	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042114	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042115	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11042116	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11042118	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11042127	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs12049908	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12418190	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16906256	0.80[YRI][hapmap]
rs2163626	0.81[CEU][hapmap]
rs2455601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653559	0.85[CEU][hapmap]
rs3751064	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs3763913	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs3763914	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs56336128	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7104661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72632952	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12223690	TMEM9B-AS1	cis	lung	GTEx
rs12223690	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs12223690	TMEM9B-AS1	cis	Thyroid	GTEx
rs12223690	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs12223690	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs12223690	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs12223690	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8892800-8906600	Weak transcription	Spleen	Spleen
2	chr11:8894000-8903400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:8901000-8908000	Weak transcription	Psoas Muscle	Psoas
4	chr11:8901800-8905000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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