Variant report

Variant	rs13012289
Chromosome Location	chr2:55648437-55648438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr2:55646315-55648449	GM12878	blood:	n/a	chr2:55647260-55647276
2	MXI1	chr2:55644654-55648547	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
2	chr2:55458950..55461087-chr2:55647562..55649544,2	K562	blood:
3	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:
4	chr2:55645285..55648583-chr2:55745099..55748276,4	K562	blood:
5	chr2:55508669..55511212-chr2:55645960..55648569,3	MCF-7	breast:
6	chr2:55645285..55648583-chr2:55744780..55749543,7	K562	blood:
7	chr2:55508571..55512777-chr2:55645734..55648780,3	K562	blood:

No data

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000143947	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000163001	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11684805	1.00[AFR][1000 genomes]
rs12992823	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55647400-55648800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:55647600-55648800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:55647800-55648800	Enhancers	Fetal Brain Male	brain
4	chr2:55647800-55652400	Weak transcription	Stomach Mucosa	stomach
5	chr2:55648000-55648600	Enhancers	Primary T cells fromperipheralblood	blood
6	chr2:55648000-55648600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr2:55648000-55648600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr2:55648000-55648600	Enhancers	Brain Angular Gyrus	brain
9	chr2:55648000-55648600	Enhancers	Brain Hippocampus Middle	brain
10	chr2:55648000-55648600	Enhancers	K562	blood
11	chr2:55648000-55648800	Enhancers	Primary B cells from peripheral blood	blood
12	chr2:55648000-55648800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr2:55648000-55648800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:55648000-55649000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:55648000-55649200	Weak transcription	Fetal Heart	heart
16	chr2:55648000-55649200	Enhancers	Fetal Muscle Leg	muscle
17	chr2:55648000-55649200	Enhancers	Fetal Thymus	thymus
18	chr2:55648000-55649400	Enhancers	NHDF-Ad	bronchial
19	chr2:55648000-55649800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:55648000-55649800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:55648000-55650000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:55648000-55650000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:55648000-55650000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr2:55648000-55650000	Enhancers	Brain Germinal Matrix	brain
25	chr2:55648000-55651000	Weak transcription	HMEC	breast
26	chr2:55648000-55651200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:55648000-55651600	Weak transcription	NHEK	skin
28	chr2:55648000-55652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:55648000-55652200	Weak transcription	HUVEC	blood vessel
30	chr2:55648000-55652200	Weak transcription	NH-A	brain
31	chr2:55648000-55652400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:55648000-55652400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:55648000-55652400	Weak transcription	HSMM	muscle
34	chr2:55648000-55653400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr2:55648000-55659000	Weak transcription	Adipose Nuclei	Adipose
36	chr2:55648200-55648600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr2:55648200-55648600	Flanking Active TSS	GM12878-XiMat	blood
38	chr2:55648200-55648800	Enhancers	Primary B cells from cord blood	blood
39	chr2:55648200-55648800	Flanking Active TSS	HepG2	liver
40	chr2:55648200-55650000	Enhancers	Primary hematopoietic stem cells	blood
41	chr2:55648200-55651000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:55648200-55651200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:55648200-55652200	Weak transcription	Osteobl	bone
44	chr2:55648400-55648600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:55648400-55648600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:55648400-55648600	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:55648400-55649200	Weak transcription	Fetal Lung	lung
48	chr2:55648400-55649200	Enhancers	NHLF	lung
49	chr2:55648400-55649400	Enhancers	Primary T cells from cord blood	blood
50	chr2:55648400-55649400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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