Variant report

Variant	rs2568091
Chromosome Location	chr11:8986048-8986049
allele	A/C
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	chr11:8985487-8986805	HEK293	kidney:	n/a	n/a
2	GABPA	chr11:8985525-8986754	Hela-S3	cervix:	n/a	chr11:8985970-8985979
3	POLR2A	chr11:8985124-8987161	HepG2	liver:	n/a	n/a
4	CREB1	chr11:8985448-8986892	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:8985160-8986872	GM19193	blood:	n/a	n/a
6	TCF7L2	chr11:8985728-8986802	Hela-S3	cervix:	n/a	n/a
7	STAT1	chr11:8985587-8986645	GM12878	blood:	n/a	chr11:8985596-8985608
8	BCL3	chr11:8985438-8986933	A549	lung:	n/a	chr11:8985979-8985988 chr11:8985615-8985624
9	ELK1	chr11:8985674-8986736	Hela-S3	cervix:	n/a	n/a
10	MAX	chr11:8985212-8986939	HCT-116	colon:	n/a	chr11:8986527-8986537 chr11:8985612-8985622 chr11:8986441-8986450
11	TAF1	chr11:8985506-8986799	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:8985454-8986890	Hela-S3	cervix:	n/a	n/a
13	MAX	chr11:8985216-8986868	K562	blood:	n/a	chr11:8986527-8986537 chr11:8985612-8985622 chr11:8986441-8986450
14	TBP	chr11:8985396-8986827	H1-hESC	embryonic stem cell:	n/a	n/a
15	SIN3AK20	chr11:8985854-8986201	SK-N-SH	brain:	n/a	n/a
16	YY1	chr11:8985617-8986745	SK-N-SH	brain:	n/a	chr11:8986580-8986591
17	PML	chr11:8985727-8986557	K562	blood:	n/a	n/a
18	YY1	chr11:8985856-8986759	ECC-1	luminal epithelium:	n/a	chr11:8986580-8986591
19	RFX5	chr11:8985710-8986558	GM12878	blood:	n/a	n/a
20	TAF1	chr11:8985473-8986769	ECC-1	luminal epithelium:	n/a	n/a
21	USF1	chr11:8985829-8986122	SK-N-SH_RA	brain:	n/a	n/a
22	TAF1	chr11:8985459-8986833	A549	lung:	n/a	n/a
23	KAP1	chr11:8985746-8986816	HEK293	kidney:	n/a	n/a
24	BCL3	chr11:8985580-8986671	A549	lung:	n/a	chr11:8985979-8985988 chr11:8985615-8985624
25	MAX	chr11:8985599-8986760	K562	blood:	n/a	chr11:8986527-8986537 chr11:8985612-8985622 chr11:8986441-8986450
26	ELF1	chr11:8985535-8986810	A549	lung:	n/a	n/a
27	SMARCB1	chr11:8985269-8986852	Hela-S3	cervix:	n/a	n/a
28	MYBL2	chr11:8985610-8986312	HepG2	liver:	n/a	n/a
29	POLR2A	chr11:8985595-8986818	HCT-116	colon:	n/a	n/a
30	SRF	chr11:8985644-8986811	MCF-7	breast:	n/a	n/a
31	ELK4	chr11:8985785-8986272	HEK293	kidney:	n/a	chr11:8985977-8985988
32	CREB1	chr11:8985514-8986661	H1-hESC	embryonic stem cell:	n/a	n/a
33	REST	chr11:8984906-8986990	H1-neurons	neurons:	n/a	chr11:8986327-8986337 chr11:8986331-8986344 chr11:8986535-8986548 chr11:8985496-8985505
34	E2F6	chr11:8985491-8986697	A549	lung:	n/a	chr11:8986235-8986247 chr11:8985614-8985623
35	NR2C2	chr11:8985616-8986905	Hela-S3	cervix:	n/a	chr11:8986038-8986047
36	TCF12	chr11:8985464-8986921	ECC-1	luminal epithelium:	n/a	n/a
37	BCLAF1	chr11:8985541-8986700	GM12878	blood:	n/a	chr11:8985979-8985988 chr11:8985615-8985624
38	NRF1	chr11:8985924-8986229	H1-hESC	embryonic stem cell:	n/a	chr11:8985970-8985979
39	HDAC2	chr11:8985655-8986189	HepG2	liver:	n/a	n/a
40	SP1	chr11:8985735-8986483	H1-hESC	embryonic stem cell:	n/a	chr11:8986067-8986081
41	TAF1	chr11:8985503-8986393	H1-hESC	embryonic stem cell:	n/a	n/a
42	CBX3	chr11:8985725-8986984	K562	blood:	n/a	n/a
43	YY1	chr11:8985767-8986295	A549	lung:	n/a	n/a
44	CREB1	chr11:8985624-8986302	ECC-1	luminal epithelium:	n/a	n/a
45	NFATC1	chr11:8985956-8986516	GM12878	blood:	n/a	n/a
46	STAT5A	chr11:8985756-8986198	K562	blood:	n/a	n/a
47	POLR2A	chr11:8985130-8987001	GM12892	blood:	n/a	n/a
48	POLR2A	chr11:8985506-8986906	GM12878	blood:	n/a	n/a
49	MAX	chr11:8985442-8986731	MCF-7	breast:	n/a	chr11:8986527-8986537 chr11:8985612-8985622 chr11:8986441-8986450
50	BHLHE40	chr11:8985681-8986700	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:8985527..8986080-chr3:134093190..134093971,2	Hela-S3	cervix:
2	chr11:8986015..8986534-chr16:278902..279566,2	Hela-S3	cervix:
3	chr11:8985678..8987470-chr11:8987575..8989239,2	K562	blood:
4	chr11:8985808..8986475-chr19:40502851..40503682,2	Hela-S3	cervix:
5	chr11:8983863..8986997-chr11:9158044..9162292,6	MCF-7	breast:
6	chr11:8985878..8986602-chr16:57481382..57481901,2	Hela-S3	cervix:
7	chr11:8985499..8986086-chr14:60558320..60558921,2	NB4	blood:
8	chr11:8705138..8707621-chr11:8984474..8986069,2	K562	blood:
9	chr11:8699371..8704185-chr11:8984475..8986762,4	K562	blood:
10	chr11:8985177..8988020-chr11:9331940..9333549,2	K562	blood:
11	chr11:8984349..8987280-chr11:9024480..9026486,3	K562	blood:
12	chr11:8985597..8987070-chr11:62608525..62609394,5	Hela-S3	cervix:
13	chr11:8715208..8718003-chr11:8985259..8987676,2	K562	blood:
14	chr11:8931659..8933906-chr11:8984325..8986430,2	K562	blood:
15	chr11:8986044..8986942-chr19:5690027..5690687,2	Hela-S3	cervix:

Variant related genes	Relation type
TMEM9B	TF binding region
TMEM9B-AS1	TF binding region
ENSG00000200983	Chromatin interaction
ENSG00000258553	Chromatin interaction
ENSG00000175356	Chromatin interaction
ENSG00000254860	Chromatin interaction
ENSG00000187187	Chromatin interaction
ENSG00000254900	Chromatin interaction
ENSG00000212607	Chromatin interaction
ENSG00000253973	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000088682	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000130255	Chromatin interaction
ENSG00000254884	Chromatin interaction
ENSG00000175352	Chromatin interaction
ENSG00000114019	Chromatin interaction
ENSG00000126773	Chromatin interaction
ENSG00000007392	Chromatin interaction
ENSG00000005194	Chromatin interaction
ENSG00000166452	Chromatin interaction
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10279	0.84[EUR][1000 genomes]
rs11042114	0.81[EUR][1000 genomes]
rs11042115	0.80[EUR][1000 genomes]
rs11042116	0.80[EUR][1000 genomes]
rs11042127	0.90[EUR][1000 genomes]
rs11042133	0.90[EUR][1000 genomes]
rs11042148	0.89[EUR][1000 genomes]
rs1109304	0.90[EUR][1000 genomes]
rs12049908	0.81[EUR][1000 genomes]
rs2163626	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2248245	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2316521	0.91[EUR][1000 genomes]
rs2568044	0.94[ASN][1000 genomes]
rs2568068	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568070	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568085	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568089	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568092	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2568094	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2653569	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2653573	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2742478	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742484	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742485	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751064	0.90[EUR][1000 genomes]
rs3763913	0.86[EUR][1000 genomes]
rs3763914	0.87[EUR][1000 genomes]
rs3815991	0.91[EUR][1000 genomes]
rs56680262	0.90[EUR][1000 genomes]
rs59454329	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7938995	0.82[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
rs2568091	TMEM9B-AS1	cis	Artery Aorta	GTEx
rs2568091	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs2568091	TMEM9B-AS1	cis	Heart Left Ventricle	GTEx
rs2568091	TMEM9B-AS1	cis	Nerve Tibial	GTEx
rs2568091	TMEM9B-AS1	cis	Thyroid	GTEx
rs2568091	TMEM9B-AS1	cis	Stomach	GTEx
rs2568091	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2568091	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2568091	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs2568091	TMEM9B-AS1	cis	lung	GTEx
rs2568091	TMEM9B-AS1	cis	Whole Blood	GTEx
rs2568091	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs2568091	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 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	chr11:8984600-8986600	Active TSS	K562	blood
6	chr11:8984600-8986800	Active TSS	Fetal Intestine Large	intestine
7	chr11:8984800-8986600	Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr11:8984800-8986800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr11:8984800-8986800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:8984800-8986800	Active TSS	A549	lung
11	chr11:8984800-8987200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:8984800-8987200	Active TSS	NHLF	lung
13	chr11:8985000-8986200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:8985000-8986400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:8985000-8986400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:8985000-8986600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr11:8985000-8986800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr11:8985000-8986800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:8985000-8986800	Active TSS	Aorta	Aorta
20	chr11:8985000-8987000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr11:8985000-8987000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr11:8985000-8987000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:8985000-8987000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:8985000-8987000	Active TSS	Esophagus	oesophagus
25	chr11:8985000-8987000	Active TSS	Fetal Kidney	kidney
26	chr11:8985000-8987000	Active TSS	Lung	lung
27	chr11:8985000-8987200	Active TSS	H1 Cell Line	embryonic stem cell
28	chr11:8985000-8987200	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr11:8985200-8986200	Active TSS	NHEK	skin
30	chr11:8985200-8986400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:8985200-8986400	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr11:8985200-8986400	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr11:8985200-8986400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:8985200-8986600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:8985200-8986600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:8985200-8986600	Active TSS	Colon Smooth Muscle	Colon
37	chr11:8985200-8986600	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr11:8985200-8986800	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr11:8985200-8986800	Active TSS	Fetal Intestine Small	intestine
40	chr11:8985200-8986800	Active TSS	Gastric	stomach
41	chr11:8985200-8986800	Active TSS	Ovary	ovary
42	chr11:8985200-8987000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr11:8985200-8987000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:8985200-8987000	Active TSS	Left Ventricle	heart
45	chr11:8985200-8987000	Active TSS	Pancreas	Pancrea
46	chr11:8985200-8987000	Active TSS	Small Intestine	intestine
47	chr11:8985200-8987000	Active TSS	NHDF-Ad	bronchial
48	chr11:8985200-8987200	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr11:8985200-8987200	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr11:8985200-8987200	Active TSS	iPS-20b Cell Line	embryonic stem cell

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