Variant report

Variant	rs2742485
Chromosome Location	chr11:8986787-8986788
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	chr11:8985487-8986805	HEK293	kidney:	n/a	n/a
2	POLR2A	chr11:8985124-8987161	HepG2	liver:	n/a	n/a
3	CREB1	chr11:8985448-8986892	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:8985160-8986872	GM19193	blood:	n/a	n/a
5	TCF7L2	chr11:8985728-8986802	Hela-S3	cervix:	n/a	n/a
6	BCL3	chr11:8985438-8986933	A549	lung:	n/a	chr11:8985979-8985988 chr11:8985615-8985624
7	MAX	chr11:8985212-8986939	HCT-116	colon:	n/a	chr11:8986527-8986537 chr11:8985612-8985622 chr11:8986441-8986450
8	TAF1	chr11:8985506-8986799	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:8985454-8986890	Hela-S3	cervix:	n/a	n/a
10	MAX	chr11:8985216-8986868	K562	blood:	n/a	chr11:8986527-8986537 chr11:8985612-8985622 chr11:8986441-8986450
11	TBP	chr11:8985396-8986827	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr11:8985459-8986833	A549	lung:	n/a	n/a
13	KAP1	chr11:8985746-8986816	HEK293	kidney:	n/a	n/a
14	ELF1	chr11:8985535-8986810	A549	lung:	n/a	n/a
15	SMARCB1	chr11:8985269-8986852	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr11:8985595-8986818	HCT-116	colon:	n/a	n/a
17	SRF	chr11:8985644-8986811	MCF-7	breast:	n/a	n/a
18	REST	chr11:8984906-8986990	H1-neurons	neurons:	n/a	chr11:8986327-8986337 chr11:8986331-8986344 chr11:8986535-8986548 chr11:8985496-8985505
19	NR2C2	chr11:8985616-8986905	Hela-S3	cervix:	n/a	chr11:8986038-8986047
20	TCF12	chr11:8985464-8986921	ECC-1	luminal epithelium:	n/a	n/a
21	CBX3	chr11:8985725-8986984	K562	blood:	n/a	n/a
22	POLR2A	chr11:8985130-8987001	GM12892	blood:	n/a	n/a
23	POLR2A	chr11:8985506-8986906	GM12878	blood:	n/a	n/a
24	SIN3A	chr11:8985140-8986881	H1-hESC	embryonic stem cell:	n/a	chr11:8986328-8986337 chr11:8986580-8986593 chr11:8985564-8985575 chr11:8986331-8986344 chr11:8985630-8985638
25	SIN3AK20	chr11:8985482-8986824	MCF-7	breast:	n/a	n/a
26	POLR2A	chr11:8985599-8987039	K562	blood:	n/a	n/a
27	POLR2A	chr11:8985287-8986986	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr11:8985479-8986952	PFSK-1	brain:	n/a	n/a
29	SIN3AK20	chr11:8985443-8986849	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr11:8985255-8986852	GM19099	blood:	n/a	n/a
31	SIN3AK20	chr11:8985532-8986836	A549	lung:	n/a	n/a
32	ELF1	chr11:8985395-8986946	HCT-116	colon:	n/a	n/a
33	JUND	chr11:8985622-8986822	K562	blood:	n/a	n/a
34	CTCF	chr11:8986640-8986790	HPAF	blood vessel:	n/a	chr11:8986661-8986677
35	POLR2A	chr11:8985359-8986838	ECC-1	luminal epithelium:	n/a	n/a
36	WRNIP1	chr11:8986762-8986855	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:8985470-8986986	H1-hESC	embryonic stem cell:	n/a	n/a
38	RFX5	chr11:8985704-8986883	HepG2	liver:	n/a	n/a
39	TAF1	chr11:8985478-8986789	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr11:8986660-8986810	HEEpiC	esophagus:	n/a	chr11:8986661-8986677
41	RUNX3	chr11:8985359-8986806	GM12878	blood:	n/a	n/a
42	ZNF143	chr11:8985347-8986808	Hela-S3	cervix:	n/a	chr11:8985459-8985469 chr11:8985969-8985979 chr11:8986458-8986476
43	ZKSCAN1	chr11:8985420-8986808	Hela-S3	cervix:	n/a	n/a
44	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
45	TBP	chr11:8985603-8986829	K562	blood:	n/a	n/a
46	SP1	chr11:8985556-8986790	A549	lung:	n/a	chr11:8985598-8985610 chr11:8985599-8985608 chr11:8986501-8986511 chr11:8985595-8985609 chr11:8985600-8985609 chr11:8985599-8985609 chr11:8986067-8986081 chr11:8985599-8985609 chr11:8985598-8985610 chr11:8985600-8985609 chr11:8986501-8986511
47	POLR2A	chr11:8984369-8987031	GM12891	blood:	n/a	n/a
48	POLR2A	chr11:8985555-8986791	K562	blood:	n/a	n/a
49	REST	chr11:8985598-8986903	A549	lung:	n/a	chr11:8986327-8986337 chr11:8986331-8986344 chr11:8986535-8986548
50	POLR2A	chr11:8985479-8986812	GM12892	blood:	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	chr11:8986117..8986822-chr11:18655942..18656571,2	Hela-S3	cervix:
4	chr11:8986397..8986938-chr17:57915104..57915721,2	Hela-S3	cervix:
5	chr11:8985177..8988020-chr11:9331940..9333549,2	K562	blood:
6	chr11:8984349..8987280-chr11:9024480..9026486,3	K562	blood:
7	chr11:8985597..8987070-chr11:62608525..62609394,5	Hela-S3	cervix:
8	chr11:8715208..8718003-chr11:8985259..8987676,2	K562	blood:
9	chr11:8986044..8986942-chr19:5690027..5690687,2	Hela-S3	cervix:
10	chr11:8703116..8705137-chr11:8986069..8987859,2	K562	blood:

Variant related genes	Relation type
TMEM9B-AS1	TF binding region
TMEM9B	TF binding region
ENSG00000130255	Chromatin interaction
ENSG00000175352	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000254884	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000175356	Chromatin interaction
ENSG00000254860	Chromatin interaction
ENSG00000166444	Chromatin interaction
ENSG00000179119	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000253973	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11042127	0.84[EUR][1000 genomes]
rs11042133	0.84[EUR][1000 genomes]
rs11042148	0.91[EUR][1000 genomes]
rs1109304	0.85[EUR][1000 genomes]
rs2163626	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2248245	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2316521	0.93[EUR][1000 genomes]
rs2568044	0.97[ASN][1000 genomes]
rs2568068	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2568070	0.90[ASN][1000 genomes]
rs2568085	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2568089	0.90[ASN][1000 genomes]
rs2568091	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2568092	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568094	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2653569	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2653573	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2742478	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742484	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751064	0.85[EUR][1000 genomes]
rs3763913	0.82[EUR][1000 genomes]
rs3763914	0.82[EUR][1000 genomes]
rs3815991	0.93[EUR][1000 genomes]
rs56680262	0.85[EUR][1000 genomes]
rs59454329	0.86[AMR][1000 genomes];0.96[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
rs2742485	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs2742485	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx
rs2742485	TMEM9B-AS1	cis	Heart Left Ventricle	GTEx
rs2742485	TMEM9B-AS1	cis	lung	GTEx
rs2742485	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2742485	TMEM9B-AS1	cis	Whole Blood	GTEx
rs2742485	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs2742485	TMEM9B-AS1	cis	Thyroid	GTEx
rs2742485	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2742485	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs2742485	TMEM9B-AS1	cis	Stomach	GTEx
rs2742485	TMEM9B-AS1	cis	Artery Aorta	GTEx
rs2742485	TMEM9B-AS1	cis	Nerve Tibial	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	chr11:8984600-8986800	Active TSS	Fetal Intestine Large	intestine
6	chr11:8984800-8986800	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr11:8984800-8986800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:8984800-8986800	Active TSS	A549	lung
9	chr11:8984800-8987200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:8984800-8987200	Active TSS	NHLF	lung
11	chr11:8985000-8986800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr11:8985000-8986800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:8985000-8986800	Active TSS	Aorta	Aorta
14	chr11:8985000-8987000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr11:8985000-8987000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr11:8985000-8987000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:8985000-8987000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:8985000-8987000	Active TSS	Esophagus	oesophagus
19	chr11:8985000-8987000	Active TSS	Fetal Kidney	kidney
20	chr11:8985000-8987000	Active TSS	Lung	lung
21	chr11:8985000-8987200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr11:8985000-8987200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr11:8985200-8986800	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr11:8985200-8986800	Active TSS	Fetal Intestine Small	intestine
25	chr11:8985200-8986800	Active TSS	Gastric	stomach
26	chr11:8985200-8986800	Active TSS	Ovary	ovary
27	chr11:8985200-8987000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:8985200-8987000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:8985200-8987000	Active TSS	Left Ventricle	heart
30	chr11:8985200-8987000	Active TSS	Pancreas	Pancrea
31	chr11:8985200-8987000	Active TSS	Small Intestine	intestine
32	chr11:8985200-8987000	Active TSS	NHDF-Ad	bronchial
33	chr11:8985200-8987200	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr11:8985200-8987200	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr11:8985200-8987200	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr11:8985200-8987200	Active TSS	HSMM	muscle
37	chr11:8985400-8986800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:8985400-8986800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr11:8985400-8986800	Active TSS	Primary T cells from cord blood	blood
40	chr11:8985400-8986800	Active TSS	Brain Angular Gyrus	brain
41	chr11:8985400-8986800	Active TSS	Brain Cingulate Gyrus	brain
42	chr11:8985400-8986800	Active TSS	Brain Hippocampus Middle	brain
43	chr11:8985400-8986800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr11:8985400-8986800	Active TSS	Fetal Heart	heart
45	chr11:8985400-8986800	Active TSS	Placenta Amnion	Placenta Amnion
46	chr11:8985400-8986800	Active TSS	Rectal Smooth Muscle	rectum
47	chr11:8985400-8986800	Active TSS	Spleen	Spleen
48	chr11:8985400-8986800	Active TSS	HSMMtube	muscle
49	chr11:8985400-8987000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:8985400-8987000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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