Variant report

Variant	rs12808972
Chromosome Location	chr11:120057972-120057973
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	MYC	chr11:120057867-120058278	HepG2	liver:	n/a	chr11:120057927-120057940 chr11:120057928-120057939 chr11:120057924-120057943 chr11:120057929-120057938
2	EP300	chr11:120057577-120057998	GM12878	blood:	n/a	chr11:120057663-120057672
3	BATF	chr11:120057514-120058006	GM12878	blood:	n/a	n/a
4	EBF1	chr11:120057373-120058044	GM12878	blood:	n/a	chr11:120057627-120057637 chr11:120057627-120057636 chr11:120057626-120057637
5	FOXP2	chr11:120057911-120058430	SK-N-MC	brain:	n/a	n/a
6	PAX5	chr11:120057699-120057982	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:120057797-120057987	GM12878	blood:	n/a	n/a
8	EBF1	chr11:120057089-120058070	GM12878	blood:	n/a	chr11:120057627-120057637 chr11:120057627-120057636 chr11:120057626-120057637
9	MTA3	chr11:120057376-120058005	GM12878	blood:	n/a	n/a
10	PAX5	chr11:120057558-120058080	GM12878	blood:	n/a	n/a
11	EBF1	chr11:120057398-120058017	GM12878	blood:	n/a	chr11:120057627-120057637 chr11:120057627-120057636 chr11:120057626-120057637
12	IRF4	chr11:120057636-120058038	GM12878	blood:	n/a	n/a
13	USF1	chr11:120057779-120058020	HepG2	liver:	n/a	chr11:120057928-120057939
14	USF2	chr11:120057644-120058114	GM12878	blood:	n/a	n/a
15	TBP	chr11:120057726-120058172	HepG2	liver:	n/a	n/a
16	PAX5	chr11:120057456-120058130	GM12878	blood:	n/a	n/a
17	MAFK	chr11:120057584-120058128	HepG2	liver:	n/a	chr11:120057750-120057766 chr11:120057751-120057765 chr11:120057752-120057761 chr11:120057748-120057768
18	PAX5	chr11:120057531-120058053	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:120057735-120058048	HepG2	liver:	n/a	n/a
20	RELA	chr11:120057367-120058001	GM18951	blood:	n/a	n/a
21	RELA	chr11:120057485-120058010	GM19099	blood:	n/a	n/a
22	MAX	chr11:120057461-120058078	GM12878	blood:	n/a	chr11:120057927-120057940 chr11:120057928-120057939 chr11:120057924-120057943 chr11:120057929-120057938
23	POLR2A	chr11:120055424-120058056	HepG2	liver:	n/a	n/a
24	MAFF	chr11:120057575-120058282	HepG2	liver:	n/a	chr11:120057751-120057765 chr11:120057752-120057770
25	MAX	chr11:120057487-120058168	HepG2	liver:	n/a	chr11:120057927-120057940 chr11:120057928-120057939 chr11:120057924-120057943 chr11:120057929-120057938
26	FOXA1	chr11:120057850-120058381	HepG2	liver:	n/a	n/a
27	TBL1XR1	chr11:120057486-120058147	GM12878	blood:	n/a	n/a
28	BHLHE40	chr11:120057486-120058102	GM12878	blood:	n/a	n/a
29	EP300	chr11:120057479-120058010	GM12878	blood:	n/a	chr11:120057663-120057672

Variant related genes	Relation type
TRIM29	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11217712	0.86[EUR][1000 genomes]
rs12790585	0.88[AMR][1000 genomes]
rs12791282	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12791393	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12792820	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12795599	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12799647	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12800456	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12802402	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12802652	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12807240	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12807541	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12808627	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2076765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35652094	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs880487	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

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120049400-120059800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr11:120052200-120058200	Weak transcription	Fetal Brain Female	brain
3	chr11:120052600-120058200	Enhancers	Fetal Lung	lung
4	chr11:120053800-120058000	Enhancers	NHDF-Ad	bronchial
5	chr11:120055400-120058200	Enhancers	Stomach Mucosa	stomach
6	chr11:120055400-120058800	Enhancers	NHLF	lung
7	chr11:120055400-120059400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:120055600-120058400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:120055600-120059000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:120055800-120058400	Enhancers	Fetal Brain Male	brain
11	chr11:120055800-120058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:120055800-120059000	Enhancers	Small Intestine	intestine
13	chr11:120055800-120059400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:120056000-120058200	Enhancers	Spleen	Spleen
15	chr11:120056000-120058600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:120056000-120060200	Enhancers	Ovary	ovary
17	chr11:120056000-120064600	Enhancers	Fetal Stomach	stomach
18	chr11:120056200-120058000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:120056200-120058200	Enhancers	Liver	Liver
20	chr11:120056200-120058200	Enhancers	Fetal Intestine Small	intestine
21	chr11:120056200-120058200	Enhancers	Fetal Muscle Leg	muscle
22	chr11:120056200-120058800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:120056200-120059200	Enhancers	Fetal Intestine Large	intestine
24	chr11:120056200-120060800	Enhancers	Pancreas	Pancrea
25	chr11:120056400-120058200	Enhancers	Fetal Muscle Trunk	muscle
26	chr11:120056400-120059000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr11:120056400-120060200	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr11:120056600-120058000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:120056600-120058200	Enhancers	Colon Smooth Muscle	Colon
30	chr11:120056600-120058200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr11:120056800-120058600	Enhancers	Brain Anterior Caudate	brain
32	chr11:120056800-120059600	Enhancers	Duodenum Mucosa	Duodenum
33	chr11:120057000-120058000	Enhancers	Left Ventricle	heart
34	chr11:120057000-120058000	Enhancers	Right Atrium	heart
35	chr11:120057000-120058200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:120057000-120058200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:120057000-120058200	Enhancers	Right Ventricle	heart
38	chr11:120057000-120058400	Enhancers	GM12878-XiMat	blood
39	chr11:120057000-120058600	Enhancers	Esophagus	oesophagus
40	chr11:120057000-120059400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr11:120057200-120058000	Enhancers	Lung	lung
42	chr11:120057200-120058000	Enhancers	NHEK	skin
43	chr11:120057200-120058400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:120057200-120058400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:120057200-120058400	Weak transcription	Brain Germinal Matrix	brain
46	chr11:120057200-120058400	Enhancers	Brain Hippocampus Middle	brain
47	chr11:120057200-120058600	Enhancers	Brain Cingulate Gyrus	brain
48	chr11:120057400-120058200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr11:120057400-120058200	Enhancers	Gastric	stomach
50	chr11:120057400-120058200	Enhancers	NH-A	brain

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