Variant report

Variant	rs55820451
Chromosome Location	chr12:123568991-123568992
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:3)
LncRNA
region (count:1)
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	POLR2A	chr12:123568811-123569083	GM12878	blood:	n/a	n/a
2	MTA3	chr12:123567879-123569132	GM12878	blood:	n/a	n/a
3	POU2F2	chr12:123568647-123569060	GM12891	blood:	n/a	chr12:123568814-123568827
4	ZNF143	chr12:123568958-123569017	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:123568650-123569194	Raji	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123559703..123562585-chr12:123566918..123569407,2	K562	blood:
2	chr12:123558779..123562598-chr12:123568640..123572609,6	MCF-7	breast:
3	chr12:123568355..123570038-chr12:123635637..123637696,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARL6IP4-1	chr12:123568859-123569285	NONHSAT031564

No data

Variant related genes	Relation type
PITPNM2	TF binding region
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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55992397	0.82[AFR][1000 genomes]
rs56846082	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57178349	0.80[AFR][1000 genomes]
rs58282663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58490757	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59995499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60167440	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60200203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60235187	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60320128	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60424338	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60546720	0.82[AFR][1000 genomes]
rs60894374	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61089898	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61110645	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61396549	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411090	0.80[AFR][1000 genomes]
rs73411093	0.81[AFR][1000 genomes]
rs73413223	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413226	0.80[AFR][1000 genomes]
rs73413228	0.80[AFR][1000 genomes]
rs73413230	0.80[AFR][1000 genomes]
rs73413241	0.80[AFR][1000 genomes]
rs73413246	0.80[AFR][1000 genomes]
rs7964036	0.80[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:86 , 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	chr12:123561600-123569800	Weak transcription	HSMM	muscle
6	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
7	chr12:123562000-123569000	Weak transcription	HepG2	liver
8	chr12:123562000-123569400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:123562000-123576200	Weak transcription	Primary T cells from cord blood	blood
10	chr12:123562200-123572600	Weak transcription	K562	blood
11	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:123563600-123570200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:123565000-123571400	Enhancers	Fetal Heart	heart
14	chr12:123565000-123571800	Enhancers	Right Ventricle	heart
15	chr12:123565600-123571000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:123566400-123570200	Enhancers	HMEC	breast
17	chr12:123566400-123571600	Enhancers	Right Atrium	heart
18	chr12:123566400-123572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:123566600-123569000	Enhancers	Spleen	Spleen
20	chr12:123566600-123571600	Enhancers	Lung	lung
21	chr12:123566800-123569600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:123567200-123569400	Genic enhancers	Thymus	Thymus
23	chr12:123567200-123570200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:123567200-123570800	Enhancers	Liver	Liver
25	chr12:123567200-123570800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr12:123567400-123570200	Enhancers	A549	lung
27	chr12:123567400-123588000	Enhancers	Left Ventricle	heart
28	chr12:123567600-123569000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:123567800-123571600	Enhancers	Fetal Muscle Leg	muscle
30	chr12:123568000-123569000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:123568000-123569000	Flanking Active TSS	GM12878-XiMat	blood
32	chr12:123568000-123569000	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr12:123568000-123569200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr12:123568000-123570000	Enhancers	Primary T cells fromperipheralblood	blood
35	chr12:123568000-123570200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:123568000-123570600	Enhancers	Psoas Muscle	Psoas
37	chr12:123568000-123570800	Enhancers	Fetal Muscle Trunk	muscle
38	chr12:123568000-123571000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr12:123568000-123571400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:123568000-123571400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr12:123568200-123569000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:123568200-123569000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr12:123568200-123569200	Enhancers	Adipose Nuclei	Adipose
44	chr12:123568200-123569400	Enhancers	Rectal Smooth Muscle	rectum
45	chr12:123568200-123569600	Weak transcription	Hela-S3	cervix
46	chr12:123568200-123569800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:123568200-123569800	Enhancers	Ovary	ovary
48	chr12:123568200-123570800	Enhancers	Stomach Smooth Muscle	stomach
49	chr12:123568200-123571200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:123568200-123571400	Enhancers	Brain Anterior Caudate	brain

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