Variant report

Variant	rs55992397
Chromosome Location	chr12:123567172-123567173
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	CEBPB	chr12:123567166-123567502	A549	lung:	n/a	chr12:123567336-123567347
2	NR3C1	chr12:123567137-123567502	A549	lung:	n/a	n/a
3	CEBPB	chr12:123567157-123567521	Hela-S3	cervix:	n/a	chr12:123567336-123567347
4	CEBPB	chr12:123567159-123567488	K562	blood:	n/a	chr12:123567336-123567347
5	NR3C1	chr12:123567086-123567576	A549	lung:	n/a	n/a
6	NR3C1	chr12:123567159-123567505	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123559703..123562585-chr12:123566918..123569407,2	K562	blood:

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000251497	TF binding region
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11061578	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12229712	0.89[AFR][1000 genomes]
rs4427600	0.80[AFR][1000 genomes]
rs55796417	0.89[AFR][1000 genomes]
rs55820451	0.82[AFR][1000 genomes]
rs55830208	0.89[AFR][1000 genomes]
rs56020503	0.89[AFR][1000 genomes]
rs56140750	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56288804	0.81[AFR][1000 genomes]
rs56725866	0.89[AFR][1000 genomes]
rs56846082	0.80[AFR][1000 genomes]
rs57106451	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57178349	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57641050	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57719471	1.00[AMR][1000 genomes]
rs57764857	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57794792	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58282663	0.82[AFR][1000 genomes]
rs58339539	0.85[AMR][1000 genomes]
rs59379557	0.81[AFR][1000 genomes]
rs59615440	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59881907	1.00[AMR][1000 genomes]
rs59995499	0.80[AFR][1000 genomes]
rs60167440	0.80[AFR][1000 genomes]
rs60200203	0.82[AFR][1000 genomes]
rs60235187	0.80[AFR][1000 genomes]
rs60320128	0.80[AFR][1000 genomes]
rs60341839	0.89[AFR][1000 genomes]
rs60341983	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60358140	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60424338	0.80[AFR][1000 genomes]
rs60546720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60761837	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60809882	0.89[AFR][1000 genomes]
rs60894374	0.80[AFR][1000 genomes]
rs60987910	0.81[AFR][1000 genomes]
rs61089898	0.80[AFR][1000 genomes]
rs61377358	0.89[AFR][1000 genomes]
rs61396549	0.80[AFR][1000 genomes]
rs61516893	0.89[AFR][1000 genomes]
rs61592192	0.81[AFR][1000 genomes]
rs61677786	0.81[AFR][1000 genomes]
rs7302112	1.00[AMR][1000 genomes]
rs73411027	0.81[AFR][1000 genomes]
rs73411033	0.81[AFR][1000 genomes]
rs73411041	0.81[AFR][1000 genomes]
rs73411043	0.81[AFR][1000 genomes]
rs73411057	0.89[AFR][1000 genomes]
rs73411058	0.89[AFR][1000 genomes]
rs73411063	0.89[AFR][1000 genomes]
rs73411076	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411084	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411087	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411088	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411090	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411093	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411098	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73413223	0.80[AFR][1000 genomes]
rs73413226	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413228	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413230	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413236	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413241	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413246	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413263	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413265	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413270	1.00[AMR][1000 genomes]
rs73417317	0.85[AMR][1000 genomes]
rs73417324	0.85[AMR][1000 genomes]
rs752164	0.89[AFR][1000 genomes]
rs7952760	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7964036	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS 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 miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123560200-123570400	Weak transcription	Aorta	Aorta
2	chr12:123560600-123574200	Weak transcription	Gastric	stomach
3	chr12:123560800-123568000	Weak transcription	Colonic Mucosa	Colon
4	chr12:123561000-123578800	Weak transcription	Fetal Intestine Large	intestine
5	chr12:123561200-123590000	Weak transcription	Fetal Intestine Small	intestine
6	chr12:123561400-123568400	Weak transcription	HSMMtube	muscle
7	chr12:123561600-123568200	Weak transcription	NHEK	skin
8	chr12:123561600-123569800	Weak transcription	HSMM	muscle
9	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
10	chr12:123561800-123568000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:123562000-123568000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:123562000-123568400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:123562000-123568800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:123562000-123569000	Weak transcription	HepG2	liver
15	chr12:123562000-123569400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:123562000-123576200	Weak transcription	Primary T cells from cord blood	blood
17	chr12:123562200-123567400	Weak transcription	A549	lung
18	chr12:123562200-123568200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:123562200-123572600	Weak transcription	K562	blood
20	chr12:123562400-123567200	Weak transcription	Liver	Liver
21	chr12:123562400-123568400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:123562600-123567200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:123562600-123568200	Weak transcription	Placenta	Placenta
25	chr12:123562600-123568400	Weak transcription	Brain Substantia Nigra	brain
26	chr12:123562800-123568000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:123563200-123568200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:123563400-123567200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:123563400-123568200	Weak transcription	Brain Anterior Caudate	brain
30	chr12:123563400-123568200	Weak transcription	Fetal Stomach	stomach
31	chr12:123563600-123568200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:123563600-123570200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:123563800-123567800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr12:123563800-123568000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:123563800-123568200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:123563800-123568200	Weak transcription	Brain Angular Gyrus	brain
37	chr12:123563800-123568200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:123563800-123568400	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:123563800-123568400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:123565000-123568400	Enhancers	Primary B cells from peripheral blood	blood
41	chr12:123565000-123571400	Enhancers	Fetal Heart	heart
42	chr12:123565000-123571800	Enhancers	Right Ventricle	heart
43	chr12:123565400-123568400	Enhancers	Primary B cells from cord blood	blood
44	chr12:123565600-123571000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr12:123566200-123567400	Weak transcription	GM12878-XiMat	blood
46	chr12:123566400-123570200	Enhancers	HMEC	breast
47	chr12:123566400-123571600	Enhancers	Right Atrium	heart
48	chr12:123566400-123572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:123566600-123568200	Enhancers	Hela-S3	cervix
50	chr12:123566600-123568600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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