Variant report

Variant	rs2653573
Chromosome Location	chr11:8989874-8989875
allele	C/G
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	POLR2A	chr11:8989828-8989962	K562	blood:	n/a	n/a
2	POLR2A	chr11:8989773-8989889	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8985143..8987459-chr11:8988827..8990567,2	MCF-7	breast:
2	chr11:8989184..8992438-chr11:8993740..8997240,3	MCF-7	breast:

Variant related genes	Relation type
TMEM9B	TF binding region
ENSG00000175348	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2163626	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2248245	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2568044	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2568068	0.90[ASN][1000 genomes]
rs2568070	0.90[ASN][1000 genomes]
rs2568085	0.90[ASN][1000 genomes]
rs2568089	0.90[ASN][1000 genomes]
rs2568091	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2568092	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2568094	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2653569	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742478	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2742484	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2742485	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59454329	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2653573	TMEM9B-AS1	cis	Heart Left Ventricle	GTEx
rs2653573	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs2653573	TMEM9B-AS1	cis	Stomach	GTEx
rs2653573	TMEM9B-AS1	cis	lung	GTEx
rs2653573	TMEM9B-AS1	cis	Thyroid	GTEx
rs2653573	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs2653573	TMEM9B-AS1	cis	Nerve Tibial	GTEx
rs2653573	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2653573	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs2653573	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8986800-8993600	Weak transcription	Aorta	Aorta
2	chr11:8986800-8994400	Weak transcription	Ovary	ovary
3	chr11:8986800-8995000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:8986800-8996600	Weak transcription	Spleen	Spleen
5	chr11:8987000-8990000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:8987000-8990000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:8987000-8990000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr11:8987000-8990000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr11:8987000-8990000	Weak transcription	Adipose Nuclei	Adipose
10	chr11:8987000-8990800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:8987000-8990800	Weak transcription	Thymus	Thymus
12	chr11:8987000-8991000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:8987000-8991200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:8987000-8991600	Weak transcription	Lung	lung
15	chr11:8987000-8992400	Weak transcription	Esophagus	oesophagus
16	chr11:8987000-8993600	Weak transcription	Left Ventricle	heart
17	chr11:8987000-8994200	Weak transcription	Psoas Muscle	Psoas
18	chr11:8987000-8994800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:8987000-8995000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:8987000-9007200	Weak transcription	Brain Germinal Matrix	brain
21	chr11:8987000-9007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:8987000-9010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:8987000-9011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:8987200-8990200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:8987200-8991400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:8987200-8993800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:8987400-8992800	Weak transcription	Primary B cells from cord blood	blood
28	chr11:8987600-8990400	Weak transcription	Fetal Intestine Large	intestine
29	chr11:8987600-8990400	Weak transcription	A549	lung
30	chr11:8987600-8992000	Weak transcription	Fetal Kidney	kidney
31	chr11:8987600-8992200	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:8987600-8993400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:8987600-9005000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:8987600-9006400	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:8987600-9010000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:8987600-9010000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr11:8987800-8990000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:8987800-8990000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:8987800-8990200	Weak transcription	Fetal Heart	heart
40	chr11:8987800-8990200	Weak transcription	Pancreas	Pancrea
41	chr11:8987800-8990400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:8987800-8990400	Weak transcription	Brain Substantia Nigra	brain
43	chr11:8987800-8991000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:8987800-8991000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr11:8987800-8993200	Weak transcription	Liver	Liver
46	chr11:8987800-8993200	Weak transcription	Right Ventricle	heart
47	chr11:8987800-8994400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr11:8987800-8994400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:8987800-8999000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:8987800-9005000	Weak transcription	Brain Angular Gyrus	brain

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