Variant report

Variant	rs2653569
Chromosome Location	chr11:8986978-8986979
allele	A/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	chr11:8985124-8987161	HepG2	liver:	n/a	n/a
2	REST	chr11:8984906-8986990	H1-neurons	neurons:	n/a	chr11:8986327-8986337 chr11:8986331-8986344 chr11:8986535-8986548 chr11:8985496-8985505
3	CBX3	chr11:8985725-8986984	K562	blood:	n/a	n/a
4	POLR2A	chr11:8985130-8987001	GM12892	blood:	n/a	n/a
5	POLR2A	chr11:8985599-8987039	K562	blood:	n/a	n/a
6	POLR2A	chr11:8985287-8986986	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr11:8985470-8986986	H1-hESC	embryonic stem cell:	n/a	n/a
8	EGR1	chr11:8985453-8987001	HCT-116	colon:	n/a	chr11:8986440-8986450 chr11:8985614-8985624 chr11:8986440-8986449 chr11:8986439-8986452 chr11:8986439-8986452 chr11:8986439-8986452 chr11:8986434-8986456 chr11:8986236-8986250 chr11:8986240-8986250 chr11:8986440-8986451 chr11:8986438-8986452 chr11:8986439-8986452 chr11:8986440-8986450
9	POLR2A	chr11:8984369-8987031	GM12891	blood:	n/a	n/a
10	JUN	chr11:8984993-8987016	K562	blood:	n/a	n/a
11	POLR2A	chr11:8985236-8987018	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr11:8985148-8987141	K562	blood:	n/a	n/a
13	POLR2A	chr11:8985207-8987031	Raji	blood:	n/a	n/a
14	POLR2A	chr11:8985502-8987024	U87	brain:	n/a	n/a
15	POLR2A	chr11:8985353-8987011	U87	brain:	n/a	n/a
16	POLR2A	chr11:8985359-8987011	U87	brain:	n/a	n/a
17	POLR2A	chr11:8985325-8987014	SK-N-MC	brain:	n/a	n/a
18	MXI1	chr11:8984441-8987169	SK-N-SH	brain:	n/a	n/a
19	SREBP1	chr11:8985568-8987171	GM12878	blood:	n/a	n/a
20	HCFC1	chr11:8985265-8987140	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr11:8985308-8987133	PANC-1	pancreas:	n/a	n/a
22	MAX	chr11:8985383-8987027	A549	lung:	n/a	chr11:8986527-8986537 chr11:8985612-8985622 chr11:8986441-8986450
23	MXI1	chr11:8985188-8987107	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:8985678..8987470-chr11:8987575..8989239,2	K562	blood:
2	chr11:8983863..8986997-chr11:9158044..9162292,6	MCF-7	breast:
3	chr11:8985177..8988020-chr11:9331940..9333549,2	K562	blood:
4	chr11:8984349..8987280-chr11:9024480..9026486,3	K562	blood:
5	chr11:8985597..8987070-chr11:62608525..62609394,5	Hela-S3	cervix:
6	chr11:8715208..8718003-chr11:8985259..8987676,2	K562	blood:
7	chr11:8703116..8705137-chr11:8986069..8987859,2	K562	blood:

Variant related genes	Relation type
TMEM9B	TF binding region
TMEM9B-AS1	TF binding region
ENSG00000166441	Chromatin interaction
ENSG00000254884	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000175356	Chromatin interaction
ENSG00000175352	Chromatin interaction
ENSG00000166444	Chromatin interaction
ENSG00000254860	Chromatin interaction
ENSG00000253973	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10840135	0.81[MEX][hapmap]
rs11042104	0.81[MEX][hapmap]
rs11042148	0.90[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs16906256	0.81[MEX][hapmap]
rs2116510	0.89[YRI][hapmap]
rs2116511	0.89[YRI][hapmap]
rs2163626	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2248245	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2568025	0.86[MEX][hapmap]
rs2568031	0.81[MEX][hapmap]
rs2568032	0.80[MEX][hapmap]
rs2568044	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568068	0.86[ASN][1000 genomes]
rs2568069	0.89[YRI][hapmap]
rs2568070	0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2568081	0.89[YRI][hapmap]
rs2568085	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs2568089	0.86[ASN][1000 genomes]
rs2568091	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2568092	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]
rs2568094	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2653559	0.82[JPT][hapmap]
rs2653573	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2653604	0.89[YRI][hapmap]
rs2742478	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2742484	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2742485	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2742487	0.89[YRI][hapmap]
rs2742488	0.89[YRI][hapmap]
rs2742491	0.89[YRI][hapmap]
rs2742493	0.89[YRI][hapmap]
rs3763913	0.87[MKK][hapmap]
rs3763914	0.82[TSI][hapmap]
rs3815991	0.90[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs59454329	0.81[AMR][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
rs2653569	C11orf17	cis	lymphoblastoid	seeQTL
rs2653569	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2653569	TMEM9B-AS1	cis	Heart Left Ventricle	GTEx
rs2653569	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs2653569	MMP26	cis	cerebellum	SCAN
rs2653569	EIF4G2	cis	cerebellum	SCAN
rs2653569	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs2653569	TMEM9B-AS1	cis	Stomach	GTEx
rs2653569	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs2653569	TMEM9B-AS1	cis	lung	GTEx
rs2653569	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2653569	TMEM9B-AS1	cis	Nerve Tibial	GTEx
rs2653569	TMEM9B-AS1	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8982800-8987000	Active TSS	GM12878-XiMat	blood
2	chr11:8984200-8987000	Active TSS	Psoas Muscle	Psoas
3	chr11:8984400-8987000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr11:8984400-8987200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:8984800-8987200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:8984800-8987200	Active TSS	NHLF	lung
7	chr11:8985000-8987000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr11:8985000-8987000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr11:8985000-8987000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:8985000-8987000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:8985000-8987000	Active TSS	Esophagus	oesophagus
12	chr11:8985000-8987000	Active TSS	Fetal Kidney	kidney
13	chr11:8985000-8987000	Active TSS	Lung	lung
14	chr11:8985000-8987200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr11:8985000-8987200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr11:8985200-8987000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:8985200-8987000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:8985200-8987000	Active TSS	Left Ventricle	heart
19	chr11:8985200-8987000	Active TSS	Pancreas	Pancrea
20	chr11:8985200-8987000	Active TSS	Small Intestine	intestine
21	chr11:8985200-8987000	Active TSS	NHDF-Ad	bronchial
22	chr11:8985200-8987200	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr11:8985200-8987200	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr11:8985200-8987200	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr11:8985200-8987200	Active TSS	HSMM	muscle
26	chr11:8985400-8987000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:8985400-8987000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:8985400-8987000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:8985400-8987000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:8985400-8987000	Active TSS	Brain Substantia Nigra	brain
31	chr11:8985400-8987000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr11:8985400-8987000	Active TSS	Placenta	Placenta
33	chr11:8985400-8987000	Active TSS	Right Ventricle	heart
34	chr11:8985400-8987200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:8985400-8987400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:8985600-8987000	Active TSS	Colonic Mucosa	Colon
37	chr11:8985600-8987000	Active TSS	Fetal Stomach	stomach
38	chr11:8986200-8987000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr11:8986200-8987000	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr11:8986200-8987000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr11:8986200-8987400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:8986400-8987000	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr11:8986400-8987000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr11:8986400-8987000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr11:8986400-8987000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr11:8986400-8987000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr11:8986400-8987000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr11:8986400-8987000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:8986400-8987000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:8986400-8987000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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