Variant report

Variant	rs2444239
Chromosome Location	chr11:120056416-120056417
allele	A/T
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	chr11:120054324-120056805	HepG2	liver:	n/a	n/a
2	TEAD4	chr11:120055502-120056654	HepG2	liver:	n/a	chr11:120055682-120055691
3	HDAC2	chr11:120055684-120056419	HepG2	liver:	n/a	n/a
4	EP300	chr11:120056089-120056533	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr11:120056016-120056437	SK-N-SH_RA	brain:	n/a	n/a
6	RAD21	chr11:120056152-120056497	SK-N-SH_RA	brain:	n/a	n/a
7	EP300	chr11:120055665-120056558	HepG2	liver:	n/a	n/a
8	CEBPB	chr11:120055797-120056426	HepG2	liver:	n/a	n/a
9	MAZ	chr11:120055732-120056518	HepG2	liver:	n/a	n/a
10	TCF12	chr11:120055695-120056485	HepG2	liver:	n/a	n/a
11	TBP	chr11:120055769-120056584	HepG2	liver:	n/a	n/a
12	ARID3A	chr11:120055788-120056566	HepG2	liver:	n/a	n/a
13	HNF4G	chr11:120055627-120056597	HepG2	liver:	n/a	chr11:120056354-120056368 chr11:120056353-120056368 chr11:120056352-120056370 chr11:120056353-120056368 chr11:120056353-120056368 chr11:120056355-120056367
14	MYC	chr11:120055598-120056438	HepG2	liver:	n/a	n/a
15	HEY1	chr11:120055649-120057285	HepG2	liver:	n/a	n/a
16	POLR2A	chr11:120055641-120056541	HepG2	liver:	n/a	n/a
17	POLR2A	chr11:120055162-120056941	HepG2	liver:	n/a	n/a
18	TCF7L2	chr11:120055988-120056472	HepG2	liver:	n/a	n/a
19	MAX	chr11:120055157-120056661	HepG2	liver:	n/a	chr11:120055451-120055461 chr11:120055450-120055461
20	FOXA2	chr11:120055743-120056667	HepG2	liver:	n/a	n/a
21	CEBPB	chr11:120055805-120056510	HepG2	liver:	n/a	n/a
22	POLR2A	chr11:120055886-120056582	HepG2	liver:	n/a	n/a
23	REST	chr11:120055795-120056419	HepG2	liver:	n/a	chr11:120056043-120056057
24	REST	chr11:120055724-120056501	HepG2	liver:	n/a	chr11:120056043-120056057
25	MBD4	chr11:120055842-120056570	HepG2	liver:	n/a	n/a
26	HNF4A	chr11:120055666-120056518	HepG2	liver:	n/a	chr11:120056354-120056368 chr11:120056353-120056368 chr11:120056352-120056370 chr11:120056353-120056368 chr11:120056353-120056368 chr11:120056355-120056367
27	RXRA	chr11:120055741-120056449	HepG2	liver:	n/a	n/a
28	MXI1	chr11:120055363-120056555	HepG2	liver:	n/a	chr11:120055452-120055461
29	EP300	chr11:120055654-120056622	HepG2	liver:	n/a	n/a
30	MYBL2	chr11:120055621-120056896	HepG2	liver:	n/a	n/a
31	POLR2A	chr11:120055424-120058056	HepG2	liver:	n/a	n/a
32	POLR2A	chr11:120055314-120056571	HepG2	liver:	n/a	n/a
33	NFIC	chr11:120055366-120056665	HepG2	liver:	n/a	chr11:120055744-120055761
34	HNF4A	chr11:120055681-120056641	HepG2	liver:	n/a	chr11:120056354-120056368 chr11:120056353-120056368 chr11:120056352-120056370 chr11:120056353-120056368 chr11:120056353-120056368 chr11:120056355-120056367
35	HNF4A	chr11:120055683-120056575	HepG2	liver:	n/a	chr11:120056354-120056368 chr11:120056353-120056368 chr11:120056352-120056370 chr11:120056353-120056368 chr11:120056353-120056368 chr11:120056355-120056367
36	RXRA	chr11:120055689-120056559	HepG2	liver:	n/a	n/a
37	CEBPD	chr11:120055649-120056441	HepG2	liver:	n/a	n/a
38	POLR2A	chr11:120055570-120056447	HepG2	liver:	n/a	n/a
39	HEY1	chr11:120055185-120056898	HepG2	liver:	n/a	n/a
40	HNF4G	chr11:120055718-120056566	HepG2	liver:	n/a	chr11:120056354-120056368 chr11:120056353-120056368 chr11:120056352-120056370 chr11:120056353-120056368 chr11:120056353-120056368 chr11:120056355-120056367
41	HDAC2	chr11:120055710-120056552	HepG2	liver:	n/a	n/a
42	MYBL2	chr11:120055511-120056664	HepG2	liver:	n/a	n/a
43	NFIC	chr11:120055704-120056522	HepG2	liver:	n/a	chr11:120055744-120055761
44	SP1	chr11:120055644-120056649	HepG2	liver:	n/a	chr11:120055749-120055763 chr11:120056006-120056020
45	CHD2	chr11:120055636-120056444	HepG2	liver:	n/a	n/a
46	YY1	chr11:120056258-120056516	SK-N-SH_RA	brain:	n/a	n/a
47	CEBPB	chr11:120056162-120056427	HepG2	liver:	n/a	n/a
48	EP300	chr11:120055452-120056561	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120054593..120056417-chr11:120079805..120082698,2	K562	blood:

Variant related genes	Relation type
TRIM29	TF binding region
ENSG00000184232	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10892546	0.96[ASN][1000 genomes]
rs10892547	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273399	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12278345	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790943	0.92[EUR][1000 genomes]
rs12791292	0.92[EUR][1000 genomes]
rs481599	0.96[ASN][1000 genomes]
rs507419	0.96[ASN][1000 genomes]
rs508205	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs508266	0.96[ASN][1000 genomes]
rs513638	0.96[ASN][1000 genomes]
rs7116997	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896693	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2444239	OAF	cis	Esophagus Muscularis	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120043600-120057000	Weak transcription	Esophagus	oesophagus
2	chr11:120049400-120059800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:120049600-120057000	Weak transcription	Left Ventricle	heart
4	chr11:120051600-120057600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:120051800-120057000	Weak transcription	HMEC	breast
6	chr11:120051800-120057200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:120052000-120057200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:120052000-120057400	Weak transcription	NH-A	brain
9	chr11:120052200-120058200	Weak transcription	Fetal Brain Female	brain
10	chr11:120052600-120058200	Enhancers	Fetal Lung	lung
11	chr11:120053000-120057400	Weak transcription	Brain Angular Gyrus	brain
12	chr11:120053000-120057800	Flanking Active TSS	HepG2	liver
13	chr11:120053600-120056600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:120053800-120058000	Enhancers	NHDF-Ad	bronchial
15	chr11:120054200-120057200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:120054200-120057600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:120054400-120057600	Weak transcription	Fetal Heart	heart
18	chr11:120054600-120057000	Weak transcription	Right Atrium	heart
19	chr11:120054600-120057000	Weak transcription	Right Ventricle	heart
20	chr11:120054800-120056600	Weak transcription	Colon Smooth Muscle	Colon
21	chr11:120054800-120056800	Weak transcription	Brain Anterior Caudate	brain
22	chr11:120054800-120057800	Enhancers	Fetal Kidney	kidney
23	chr11:120055400-120057400	Enhancers	Placenta	Placenta
24	chr11:120055400-120057600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:120055400-120057600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:120055400-120058200	Enhancers	Stomach Mucosa	stomach
27	chr11:120055400-120058800	Enhancers	NHLF	lung
28	chr11:120055400-120059400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:120055600-120056600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr11:120055600-120057000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:120055600-120057200	Enhancers	Brain Germinal Matrix	brain
32	chr11:120055600-120057200	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:120055600-120058400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:120055600-120059000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:120055800-120056600	Active TSS	Stomach Smooth Muscle	stomach
36	chr11:120055800-120056600	Enhancers	HSMM	muscle
37	chr11:120055800-120056800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:120055800-120057000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:120055800-120058400	Enhancers	Fetal Brain Male	brain
40	chr11:120055800-120058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr11:120055800-120059000	Enhancers	Small Intestine	intestine
42	chr11:120055800-120059400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:120056000-120056600	Active TSS	Duodenum Mucosa	Duodenum
44	chr11:120056000-120056800	Enhancers	HSMMtube	muscle
45	chr11:120056000-120058200	Enhancers	Spleen	Spleen
46	chr11:120056000-120058600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:120056000-120060200	Enhancers	Ovary	ovary
48	chr11:120056000-120064600	Enhancers	Fetal Stomach	stomach
49	chr11:120056200-120056600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:120056200-120057200	Weak transcription	Rectal Smooth Muscle	rectum

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