Variant report

Variant	rs2652596
Chromosome Location	chr15:52046359-52046360
allele	C/T
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	SPI1	chr15:52046338-52046902	HL-60	blood:	n/a	chr15:52046651-52046660

No.	Distal block	Cell Line	Cell type
1	chr15:52046348..52048954-chr15:52084849..52087226,2	K562	blood:
2	chr15:52028579..52031295-chr15:52046217..52050933,5	MCF-7	breast:
3	chr15:52028355..52032748-chr15:52040539..52046492,10	K562	blood:

Variant related genes	Relation type
LYSMD2	TF binding region
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1824083	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1867985	0.85[YRI][hapmap]
rs2162224	0.83[YRI][hapmap]
rs2554329	0.81[YRI][hapmap]
rs2554331	0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554346	0.86[YRI][hapmap]
rs2554357	0.86[YRI][hapmap]
rs2623290	0.83[YRI][hapmap]
rs543024	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs562858	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs689842	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs690433	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7179045	0.80[AFR][1000 genomes];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	esv2830011	chr15:52027777-52048710	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
2	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52044400-52046400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr15:52044400-52050800	Weak transcription	Gastric	stomach
3	chr15:52044600-52046800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr15:52044600-52060000	Weak transcription	Esophagus	oesophagus
5	chr15:52044600-52060200	Weak transcription	Aorta	Aorta
6	chr15:52044800-52046800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr15:52044800-52047600	Weak transcription	Placenta	Placenta
8	chr15:52044800-52047600	Weak transcription	Lung	lung
9	chr15:52044800-52047800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:52044800-52049800	Weak transcription	Psoas Muscle	Psoas
11	chr15:52044800-52050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:52044800-52051000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:52044800-52051000	Weak transcription	Right Ventricle	heart
14	chr15:52044800-52060000	Weak transcription	Spleen	Spleen
15	chr15:52045000-52046400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:52045000-52046800	Enhancers	Fetal Thymus	thymus
17	chr15:52045000-52047000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:52045000-52049800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:52045000-52049800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:52045000-52050600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:52045000-52050800	Weak transcription	HMEC	breast
22	chr15:52045000-52060200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:52045200-52046400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:52045200-52046400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:52045200-52046400	Enhancers	Brain Substantia Nigra	brain
26	chr15:52045200-52047400	Enhancers	Primary T cells from cord blood	blood
27	chr15:52045200-52047600	Enhancers	Dnd41	blood
28	chr15:52045200-52048200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:52045200-52049800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:52045200-52050600	Weak transcription	Brain Germinal Matrix	brain
31	chr15:52045200-52053400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr15:52045400-52047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:52045400-52048600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:52045400-52050400	Weak transcription	Fetal Brain Female	brain
35	chr15:52045400-52050600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr15:52045400-52050600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:52045400-52051000	Weak transcription	Left Ventricle	heart
38	chr15:52045600-52047600	Weak transcription	Right Atrium	heart
39	chr15:52045600-52047600	Weak transcription	K562	blood
40	chr15:52045600-52048200	Weak transcription	Adipose Nuclei	Adipose
41	chr15:52045600-52049800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:52045600-52050600	Weak transcription	Colon Smooth Muscle	Colon
43	chr15:52045800-52046400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr15:52045800-52046600	Enhancers	Brain Angular Gyrus	brain
45	chr15:52045800-52046800	Enhancers	Brain Cingulate Gyrus	brain
46	chr15:52045800-52047600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:52045800-52048000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr15:52045800-52049800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:52045800-52053200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:52046000-52046400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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