Variant report

Variant	rs2316521
Chromosome Location	chr11:9006883-9006884
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10279	0.85[ASN][1000 genomes]
rs11042127	0.82[EUR][1000 genomes]
rs11042133	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042148	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109304	0.83[EUR][1000 genomes]
rs2163626	0.84[EUR][1000 genomes]
rs2248245	0.95[EUR][1000 genomes]
rs2568091	0.91[EUR][1000 genomes]
rs2568092	0.95[EUR][1000 genomes]
rs2568094	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2742478	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2742484	0.95[EUR][1000 genomes]
rs2742485	0.93[EUR][1000 genomes]
rs3751064	0.83[EUR][1000 genomes]
rs3763913	0.80[ASN][1000 genomes]
rs3815991	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56680262	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59454329	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7938995	0.80[AMR][1000 genomes];0.84[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	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
4	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
5	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2316521	TMEM9B-AS1	cis	lung	GTEx
rs2316521	TMEM9B-AS1	cis	Stomach	GTEx
rs2316521	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs2316521	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs2316521	TMEM9B-AS1	cis	Thyroid	GTEx
rs2316521	TMEM9B-AS1	cis	Nerve Tibial	GTEx
rs2316521	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2316521	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs2316521	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs2316521	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2316521	TMEM9B-AS1	cis	Heart Left Ventricle	GTEx
rs2316521	TMEM9B-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8987000-9007200	Weak transcription	Brain Germinal Matrix	brain
2	chr11:8987000-9007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:8987000-9010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:8987000-9011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:8987600-9010000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:8987600-9010000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:8987800-9010200	Weak transcription	NHDF-Ad	bronchial
8	chr11:8987800-9012000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr11:8989600-9010000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:8989600-9011200	Weak transcription	Brain Anterior Caudate	brain
11	chr11:8989600-9019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:8991800-9015600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:8994000-9008600	Weak transcription	K562	blood
14	chr11:8999600-9009800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:9001800-9015200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:9005600-9010200	Weak transcription	HUVEC	blood vessel
17	chr11:9005600-9010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:9006600-9008200	Enhancers	HepG2	liver

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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