Variant report

Variant	rs59454329
Chromosome Location	chr11:8987003-8987004
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:8985124-8987161	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:8985599-8987039	K562	blood:	n/a	n/a
3	POLR2A	chr11:8984369-8987031	GM12891	blood:	n/a	n/a
4	JUN	chr11:8984993-8987016	K562	blood:	n/a	n/a
5	POLR2A	chr11:8985236-8987018	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr11:8985148-8987141	K562	blood:	n/a	n/a
7	POLR2A	chr11:8985207-8987031	Raji	blood:	n/a	n/a
8	POLR2A	chr11:8985502-8987024	U87	brain:	n/a	n/a
9	POLR2A	chr11:8985353-8987011	U87	brain:	n/a	n/a
10	POLR2A	chr11:8985359-8987011	U87	brain:	n/a	n/a
11	POLR2A	chr11:8985325-8987014	SK-N-MC	brain:	n/a	n/a
12	MXI1	chr11:8984441-8987169	SK-N-SH	brain:	n/a	n/a
13	SREBP1	chr11:8985568-8987171	GM12878	blood:	n/a	n/a
14	HCFC1	chr11:8985265-8987140	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr11:8985308-8987133	PANC-1	pancreas:	n/a	n/a
16	MAX	chr11:8985383-8987027	A549	lung:	n/a	chr11:8986527-8986537 chr11:8985612-8985622 chr11:8986441-8986450
17	MXI1	chr11:8985188-8987107	IMR90	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:8985678..8987470-chr11:8987575..8989239,2	K562	blood:
2	chr11:8985177..8988020-chr11:9331940..9333549,2	K562	blood:
3	chr11:8984349..8987280-chr11:9024480..9026486,3	K562	blood:
4	chr11:8985597..8987070-chr11:62608525..62609394,5	Hela-S3	cervix:
5	chr11:8715208..8718003-chr11:8985259..8987676,2	K562	blood:
6	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
ENSG00000133316	Chromatin interaction
ENSG00000175352	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000166444	Chromatin interaction
ENSG00000253973	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10279	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11042127	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11042133	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042148	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1109304	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2163626	0.87[EUR][1000 genomes]
rs2248245	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2316521	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2568091	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2568092	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568094	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2653569	0.81[AMR][1000 genomes]
rs2653573	0.80[AMR][1000 genomes]
rs2742478	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2742484	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742485	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3751064	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3763913	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3763914	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3815991	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56680262	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7938995	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs59454329	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs59454329	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs59454329	TMEM9B-AS1	cis	Stomach	GTEx
rs59454329	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs59454329	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs59454329	TMEM9B-AS1	cis	lung	GTEx
rs59454329	TMEM9B-AS1	cis	Thyroid	GTEx
rs59454329	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs59454329	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs59454329	TMEM9B-AS1	cis	Nerve Tibial	GTEx
rs59454329	TMEM9B-AS1	cis	Artery Aorta	GTEx
rs59454329	TMEM9B-AS1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8984400-8987200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:8984800-8987200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:8984800-8987200	Active TSS	NHLF	lung
4	chr11:8985000-8987200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr11:8985000-8987200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr11:8985200-8987200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr11:8985200-8987200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr11:8985200-8987200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr11:8985200-8987200	Active TSS	HSMM	muscle
10	chr11:8985400-8987200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:8985400-8987400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:8986200-8987400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:8986400-8987200	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr11:8986600-8987200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:8986600-8987200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:8986600-8987200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr11:8986600-8987200	Active TSS	HepG2	liver
18	chr11:8986800-8987200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:8986800-8987200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:8986800-8987200	Enhancers	Primary B cells from peripheral blood	blood
21	chr11:8986800-8987200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:8986800-8987200	Flanking Active TSS	Fetal Intestine Small	intestine
23	chr11:8986800-8987800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:8986800-8993600	Weak transcription	Aorta	Aorta
25	chr11:8986800-8994400	Weak transcription	Ovary	ovary
26	chr11:8986800-8995000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr11:8986800-8996600	Weak transcription	Spleen	Spleen
28	chr11:8987000-8987200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr11:8987000-8987200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:8987000-8987200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:8987000-8987200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr11:8987000-8987200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:8987000-8987200	Enhancers	Brain Angular Gyrus	brain
34	chr11:8987000-8987200	Enhancers	Brain Cingulate Gyrus	brain
35	chr11:8987000-8987200	Active TSS	Brain Hippocampus Middle	brain
36	chr11:8987000-8987200	Enhancers	Duodenum Mucosa	Duodenum
37	chr11:8987000-8987200	Weak transcription	Pancreas	Pancrea
38	chr11:8987000-8987200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr11:8987000-8987200	Weak transcription	Right Ventricle	heart
40	chr11:8987000-8987200	Enhancers	HMEC	breast
41	chr11:8987000-8987200	Enhancers	HUVEC	blood vessel
42	chr11:8987000-8987200	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr11:8987000-8987200	Weak transcription	NHDF-Ad	bronchial
44	chr11:8987000-8987400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:8987000-8987400	Enhancers	Primary B cells from cord blood	blood
46	chr11:8987000-8987400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:8987000-8987400	Weak transcription	Fetal Kidney	kidney
48	chr11:8987000-8987400	Enhancers	Fetal Muscle Trunk	muscle
49	chr11:8987000-8987400	Active TSS	Hela-S3	cervix
50	chr11:8987000-8987600	Weak transcription	H9 Cell Line	embryonic stem cell

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