Variant report

Variant	rs2568092
Chromosome Location	chr11:8987438-8987439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr11:8987414-8987486	K562	blood:	n/a	n/a
2	CUX1	chr11:8987425-8987591	K562	blood:	n/a	n/a
3	POLR2A	chr11:8987436-8988253	K562	blood:	n/a	n/a
4	POLR2A	chr11:8987420-8987634	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:8985678..8987470-chr11:8987575..8989239,2	K562	blood:
2	chr11:8703166..8704942-chr11:8987139..8989652,2	K562	blood:
3	chr11:8985177..8988020-chr11:9331940..9333549,2	K562	blood:
4	chr11:8715208..8718003-chr11:8985259..8987676,2	K562	blood:
5	chr11:8703116..8705137-chr11:8986069..8987859,2	K562	blood:

No data

Variant related genes	Relation type
TMEM9B-AS1	TF binding region
TMEM9B	TF binding region
ENSG00000254884	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000254860	Chromatin interaction
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10840135	0.80[MEX][hapmap]
rs11042104	0.80[MEX][hapmap]
rs11042127	0.85[EUR][1000 genomes]
rs11042133	0.85[EUR][1000 genomes]
rs11042148	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1109304	0.86[EUR][1000 genomes]
rs16906256	0.80[MEX][hapmap]
rs2163626	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2248245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316521	0.95[EUR][1000 genomes]
rs2568044	0.97[ASN][1000 genomes]
rs2568068	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2568070	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2568085	0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2568089	0.90[ASN][1000 genomes]
rs2568091	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2568094	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653569	0.83[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2653573	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2742478	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742485	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751064	0.86[EUR][1000 genomes]
rs3763913	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs3763914	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs3815991	1.00[CEU][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs56680262	0.86[EUR][1000 genomes]
rs59454329	0.84[AMR][1000 genomes];0.97[EUR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2568092	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs2568092	TMEM9B-AS1	cis	Whole Blood	GTEx
rs2568092	TMEM9B-AS1	cis	Nerve Tibial	GTEx
rs2568092	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs2568092	TMEM9B-AS1	cis	Heart Left Ventricle	GTEx
rs2568092	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2568092	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2568092	TMEM9B-AS1	cis	lung	GTEx
rs2568092	TMEM9B-AS1	cis	Stomach	GTEx
rs2568092	TMEM9B-AS1	cis	Artery Aorta	GTEx
rs2568092	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs2568092	TMEM9B-AS1	cis	Thyroid	GTEx
rs2568092	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8986800-8987800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr11:8986800-8993600	Weak transcription	Aorta	Aorta
3	chr11:8986800-8994400	Weak transcription	Ovary	ovary
4	chr11:8986800-8995000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:8986800-8996600	Weak transcription	Spleen	Spleen
6	chr11:8987000-8987600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:8987000-8987600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:8987000-8987600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr11:8987000-8987600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr11:8987000-8987600	Enhancers	Colon Smooth Muscle	Colon
11	chr11:8987000-8987600	Enhancers	Fetal Intestine Large	intestine
12	chr11:8987000-8987600	Enhancers	Fetal Lung	lung
13	chr11:8987000-8987600	Enhancers	A549	lung
14	chr11:8987000-8987600	Enhancers	NH-A	brain
15	chr11:8987000-8987600	Enhancers	NHEK	skin
16	chr11:8987000-8987800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:8987000-8987800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr11:8987000-8987800	Enhancers	Primary hematopoietic stem cells	blood
19	chr11:8987000-8987800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr11:8987000-8987800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:8987000-8987800	Enhancers	Liver	Liver
22	chr11:8987000-8987800	Enhancers	Brain Substantia Nigra	brain
23	chr11:8987000-8987800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr11:8987000-8987800	Enhancers	Fetal Heart	heart
25	chr11:8987000-8987800	Enhancers	Fetal Muscle Leg	muscle
26	chr11:8987000-8987800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr11:8987000-8987800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr11:8987000-8988200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:8987000-8988200	Enhancers	Dnd41	blood
30	chr11:8987000-8988600	Enhancers	K562	blood
31	chr11:8987000-8988800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr11:8987000-8988800	Enhancers	Brain Anterior Caudate	brain
33	chr11:8987000-8988800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:8987000-8988800	Weak transcription	Fetal Stomach	stomach
35	chr11:8987000-8989000	Weak transcription	Placenta	Placenta
36	chr11:8987000-8989200	Weak transcription	Primary T cells from cord blood	blood
37	chr11:8987000-8989600	Enhancers	GM12878-XiMat	blood
38	chr11:8987000-8989800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:8987000-8990000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:8987000-8990000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr11:8987000-8990000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr11:8987000-8990000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr11:8987000-8990000	Weak transcription	Adipose Nuclei	Adipose
44	chr11:8987000-8990800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:8987000-8990800	Weak transcription	Thymus	Thymus
46	chr11:8987000-8991000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:8987000-8991200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:8987000-8991600	Weak transcription	Lung	lung
49	chr11:8987000-8992400	Weak transcription	Esophagus	oesophagus
50	chr11:8987000-8993600	Weak transcription	Left Ventricle	heart

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