Variant report

Variant	rs11042098
Chromosome Location	chr11:8865179-8865180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10743091	0.92[EUR][1000 genomes]
rs10840135	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840137	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11042097	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042104	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12798322	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1368017	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16906256	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2292049	0.90[EUR][1000 genomes]
rs2568025	0.80[EUR][1000 genomes]
rs2568031	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568032	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34874636	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59025804	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61876202	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7127479	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7948452	0.84[AMR][1000 genomes];0.87[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
rs11042098	TMEM9B-AS1	cis	lung	GTEx
rs11042098	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11042098	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs11042098	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs11042098	TMEM9B-AS1	cis	Thyroid	GTEx
rs11042098	TMEM9B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8862200-8881200	Weak transcription	Hela-S3	cervix
2	chr11:8862400-8865200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:8862400-8865200	Weak transcription	Pancreas	Pancrea
4	chr11:8862400-8867000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:8862400-8867800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:8862400-8867800	Weak transcription	Ovary	ovary
7	chr11:8862400-8868000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:8862400-8868000	Weak transcription	Left Ventricle	heart
9	chr11:8862400-8870600	Weak transcription	Placenta	Placenta
10	chr11:8862400-8874600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:8862400-8880000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:8862400-8880000	Weak transcription	Spleen	Spleen
13	chr11:8862400-8885000	Weak transcription	NHLF	lung
14	chr11:8862400-8888400	Weak transcription	Right Atrium	heart
15	chr11:8862600-8865200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:8862600-8866400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:8862600-8867000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:8862600-8867800	Weak transcription	Brain Substantia Nigra	brain
19	chr11:8862600-8868400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:8862600-8868800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:8862600-8876600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:8862600-8885200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:8862800-8865400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:8863000-8866400	Weak transcription	Fetal Muscle Leg	muscle
25	chr11:8863200-8866400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:8863200-8867200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr11:8863600-8866800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:8863600-8867000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:8864000-8872200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:8864000-8888000	Weak transcription	Fetal Intestine Small	intestine
32	chr11:8864600-8865200	Weak transcription	Fetal Lung	lung
33	chr11:8864800-8865800	Enhancers	Fetal Stomach	stomach
34	chr11:8864800-8865800	Enhancers	Stomach Smooth Muscle	stomach
35	chr11:8864800-8866000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:8865000-8865400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:8865000-8865400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:8865000-8865600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:8865000-8865600	Enhancers	HUES64 Cell Line	embryonic stem cell

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