Variant report

Variant	rs10840158
Chromosome Location	chr11:9020897-9020898
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8992414..8994914-chr11:9017191..9020958,3	K562	blood:
2	chr11:9015661..9017205-chr11:9018706..9021551,2	MCF-7	breast:
3	chr11:8984509..8986856-chr11:9019529..9021120,2	K562	blood:
4	chr11:8984509..8986690-chr11:9019329..9021120,2	K562	blood:

Variant related genes	Relation type
ENSG00000175348	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10769979	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769980	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769981	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10840157	0.98[ASN][1000 genomes]
rs11042149	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11042150	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042152	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042154	0.89[ASN][1000 genomes]
rs1109305	0.83[ASN][1000 genomes]
rs1123936	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1980428	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1980429	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984791	0.86[ASN][1000 genomes]
rs2012680	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012690	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012696	0.98[ASN][1000 genomes]
rs2568020	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568045	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2653570	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653605	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742470	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2742471	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742474	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742480	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4909952	0.83[ASN][1000 genomes]
rs4910156	0.81[ASN][1000 genomes]
rs4910157	0.84[EUR][1000 genomes]
rs4910200	0.84[ASN][1000 genomes]
rs4929922	0.87[ASN][1000 genomes]
rs7479407	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7482838	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7484180	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7925728	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930026	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10840158	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs10840158	TMEM9B-AS1	cis	lung	GTEx
rs10840158	TMEM9B-AS1	cis	Stomach	GTEx
rs10840158	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs10840158	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs10840158	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs10840158	TMEM9B-AS1	cis	Thyroid	GTEx
rs10840158	TMEM9B-AS1	cis	Artery Aorta	GTEx
rs10840158	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9011000-9023200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:9011800-9023000	Weak transcription	NHDF-Ad	bronchial
3	chr11:9020200-9022800	Weak transcription	K562	blood
4	chr11:9020200-9023200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:9020200-9023200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:9020200-9023400	Weak transcription	Gastric	stomach

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