Variant report

Variant	rs12798322
Chromosome Location	chr11:8874835-8874836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10743091	0.86[EUR][1000 genomes]
rs10840135	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840137	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042097	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042098	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042104	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1368017	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16906256	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292049	0.85[EUR][1000 genomes]
rs2568031	0.85[ASN][1000 genomes]
rs2568032	0.85[ASN][1000 genomes]
rs34874636	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59025804	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61876202	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7127479	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948452	0.91[AMR][1000 genomes];0.98[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12798322	TMEM9B-AS1	cis	Thyroid	GTEx
rs12798322	TMEM9B	Cis_1M	lymphoblastoid	RTeQTL
rs12798322	TMEM9B-AS1	cis	lung	GTEx
rs12798322	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs12798322	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs12798322	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8862200-8881200	Weak transcription	Hela-S3	cervix
2	chr11:8862400-8880000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr11:8862400-8880000	Weak transcription	Spleen	Spleen
4	chr11:8862400-8885000	Weak transcription	NHLF	lung
5	chr11:8862400-8888400	Weak transcription	Right Atrium	heart
6	chr11:8862600-8876600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr11:8862600-8885200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr11:8864000-8888000	Weak transcription	Fetal Intestine Small	intestine
10	chr11:8865800-8886000	Weak transcription	Fetal Stomach	stomach
11	chr11:8868200-8876200	Weak transcription	Ovary	ovary
12	chr11:8868800-8877000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:8871000-8877000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:8872600-8876800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:8873200-8885000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:8874000-8876800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:8874200-8880400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:8874400-8875000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:8874600-8877000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:8874600-8885000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:8874800-8879000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:8874800-8880600	Weak transcription	Placenta	Placenta

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