Variant report

Variant	rs10840139
Chromosome Location	chr11:8894838-8894839
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:8894792-8895064	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ST5	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10279	0.81[EUR][1000 genomes]
rs11042105	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042106	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042107	0.98[ASN][1000 genomes]
rs11042108	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11042114	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042115	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042116	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042118	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042127	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042133	0.87[EUR][1000 genomes]
rs1109304	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12049908	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12223690	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12418190	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2163626	0.85[EUR][1000 genomes]
rs2455601	0.98[ASN][1000 genomes]
rs3751064	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3763913	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3763914	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56336128	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56680262	0.88[EUR][1000 genomes]
rs7104661	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs72632952	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10840139	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs10840139	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs10840139	TMEM9B-AS1	cis	Heart Left Ventricle	GTEx
rs10840139	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs10840139	TMEM9B-AS1	cis	Stomach	GTEx
rs10840139	TMEM9B-AS1	cis	Thyroid	GTEx
rs10840139	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs10840139	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs10840139	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs10840139	TMEM9B-AS1	cis	lung	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8892800-8895400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr11:8892800-8906600	Weak transcription	Spleen	Spleen
3	chr11:8893200-8895400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:8893200-8895400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:8893400-8895400	Enhancers	Fetal Lung	lung
6	chr11:8893400-8895600	Weak transcription	Stomach Mucosa	stomach
7	chr11:8893400-8896600	Enhancers	Fetal Stomach	stomach
8	chr11:8893600-8895800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:8893800-8895200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:8893800-8895200	Weak transcription	Fetal Intestine Small	intestine
11	chr11:8893800-8895400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:8893800-8895400	Weak transcription	Fetal Heart	heart
13	chr11:8893800-8896200	Enhancers	NHDF-Ad	bronchial
14	chr11:8894000-8895200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:8894000-8895400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:8894000-8903400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr11:8894200-8895400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:8894400-8895200	Weak transcription	Fetal Kidney	kidney
19	chr11:8894400-8895400	Weak transcription	Colon Smooth Muscle	Colon
20	chr11:8894400-8895400	Weak transcription	NHLF	lung
21	chr11:8894400-8895600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:8894600-8895200	Weak transcription	Psoas Muscle	Psoas

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