Variant report

Variant	rs56846082
Chromosome Location	chr12:123570119-123570120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL1	chr12:123570003-123570935	HCT-116	colon:	n/a	n/a
2	SP1	chr12:123570054-123570950	HCT-116	colon:	n/a	n/a
3	TCF12	chr12:123570113-123570884	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr12:123570108-123570855	SK-N-SH	brain:	n/a	n/a
5	FOSL2	chr12:123570061-123570892	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123463347..123466075-chr12:123569459..123571842,3	MCF-7	breast:
2	chr12:123569324..123574207-chr12:123574392..123579398,5	K562	blood:
3	chr12:123564490..123568285-chr12:123569418..123571923,3	MCF-7	breast:
4	chr12:123553938..123556177-chr12:123569244..123571363,2	MCF-7	breast:
5	chr12:123558779..123562598-chr12:123568640..123572609,6	MCF-7	breast:

No data

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000251497	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs4427600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55820451	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55992397	0.80[AFR][1000 genomes]
rs57178349	0.82[AFR][1000 genomes]
rs58282663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58490757	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59995499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60167440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60200203	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60235187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60320128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60424338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60546720	0.80[AFR][1000 genomes]
rs60894374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61089898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61110645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61396549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411090	0.82[AFR][1000 genomes]
rs73411093	0.81[AFR][1000 genomes]
rs73413223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413226	0.82[AFR][1000 genomes]
rs73413228	0.82[AFR][1000 genomes]
rs73413230	0.82[AFR][1000 genomes]
rs73413241	0.82[AFR][1000 genomes]
rs73413246	0.82[AFR][1000 genomes]
rs7964036	0.82[AFR][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:87 , 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	chr12:123561000-123578800	Weak transcription	Fetal Intestine Large	intestine
4	chr12:123561200-123590000	Weak transcription	Fetal Intestine Small	intestine
5	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
6	chr12:123562000-123576200	Weak transcription	Primary T cells from cord blood	blood
7	chr12:123562200-123572600	Weak transcription	K562	blood
8	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:123563600-123570200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:123565000-123571400	Enhancers	Fetal Heart	heart
11	chr12:123565000-123571800	Enhancers	Right Ventricle	heart
12	chr12:123565600-123571000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:123566400-123570200	Enhancers	HMEC	breast
14	chr12:123566400-123571600	Enhancers	Right Atrium	heart
15	chr12:123566400-123572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:123566600-123571600	Enhancers	Lung	lung
17	chr12:123567200-123570200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:123567200-123570800	Enhancers	Liver	Liver
19	chr12:123567200-123570800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr12:123567400-123570200	Enhancers	A549	lung
21	chr12:123567400-123588000	Enhancers	Left Ventricle	heart
22	chr12:123567800-123571600	Enhancers	Fetal Muscle Leg	muscle
23	chr12:123568000-123570200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:123568000-123570600	Enhancers	Psoas Muscle	Psoas
25	chr12:123568000-123570800	Enhancers	Fetal Muscle Trunk	muscle
26	chr12:123568000-123571000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:123568000-123571400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:123568000-123571400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr12:123568200-123570800	Enhancers	Stomach Smooth Muscle	stomach
30	chr12:123568200-123571200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:123568200-123571400	Enhancers	Brain Anterior Caudate	brain
32	chr12:123568400-123570400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:123568400-123570600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:123568400-123570600	Enhancers	HSMMtube	muscle
35	chr12:123568400-123571000	Enhancers	Primary hematopoietic stem cells	blood
36	chr12:123568400-123571400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr12:123568400-123571600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:123568600-123570200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr12:123568600-123570200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:123568600-123570600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:123568600-123571000	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:123568600-123578000	Weak transcription	Colonic Mucosa	Colon
43	chr12:123568800-123571600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr12:123568800-123571800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr12:123568800-123576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:123569000-123570200	Weak transcription	Stomach Mucosa	stomach
47	chr12:123569000-123570600	Enhancers	GM12878-XiMat	blood
48	chr12:123569000-123570800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:123569000-123574000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:123569200-123570400	Weak transcription	Fetal Brain Female	brain

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