Variant report

Variant	rs2623280
Chromosome Location	chr15:52213383-52213384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52212249..52214949-chr15:52220754..52223044,2	K562	blood:

Variant related genes	Relation type
ENSG00000259556	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1863429	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1972419	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1991267	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2258248	0.92[AMR][1000 genomes]
rs2554354	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2554355	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2570243	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2570265	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2593169	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2593181	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2593184	0.92[AMR][1000 genomes]
rs2623245	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2623247	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2623251	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2623263	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2623270	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2623291	0.94[AMR][1000 genomes]
rs2959296	0.90[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	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
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52177200-52213600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:52178800-52216600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:52179800-52218600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:52180400-52218200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:52181200-52221000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:52183200-52223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:52186400-52219000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:52191000-52222800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:52192800-52213600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:52193400-52227800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:52193400-52232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:52193600-52233600	Weak transcription	Fetal Brain Male	brain
14	chr15:52193800-52216200	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:52194200-52228200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:52194200-52231600	Weak transcription	Psoas Muscle	Psoas
17	chr15:52194400-52236800	Weak transcription	Fetal Kidney	kidney
18	chr15:52194400-52239000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:52196200-52234000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:52197000-52234200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:52197000-52234800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:52198400-52219000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:52200000-52213800	Weak transcription	NHLF	lung
24	chr15:52200400-52213600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr15:52200400-52220800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
27	chr15:52200600-52213600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:52200600-52213600	Weak transcription	HUVEC	blood vessel
29	chr15:52201000-52216200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:52201000-52238800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr15:52201200-52215600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:52201400-52217800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:52201800-52223000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:52202000-52230000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:52204400-52217800	Strong transcription	Fetal Intestine Small	intestine
36	chr15:52204600-52218400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr15:52204600-52224600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:52204800-52218800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:52204800-52219400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:52204800-52238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:52205200-52215400	Weak transcription	NH-A	brain
42	chr15:52206000-52215400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:52206600-52215400	Weak transcription	HepG2	liver
44	chr15:52206600-52218400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr15:52207400-52219600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:52207600-52215800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:52208000-52217400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:52208000-52217800	Strong transcription	Fetal Intestine Large	intestine
49	chr15:52208000-52218000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:52208000-52218200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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