Variant report

Variant	rs2412511
Chromosome Location	chr15:40621701-40621702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40619456..40622052-chr15:40729021..40731269,2	K562	blood:
2	chr15:40618049..40622052-chr15:40729021..40731269,3	K562	blood:
3	chr15:40616336..40620318-chr15:40620739..40624439,7	MCF-7	breast:
4	chr15:40620284..40622510-chr15:40650949..40653083,2	K562	blood:
5	chr15:40621312..40623412-chr15:40667934..40669640,2	K562	blood:
6	chr15:40619706..40623827-chr15:40624940..40628910,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12440659	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs12441303	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2004251	0.86[JPT][hapmap]
rs2118960	0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.96[ASN][1000 genomes]
rs2289328	1.00[LWK][hapmap]
rs28405635	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs934935	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv827305	chr15:40596162-40625922	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2412511	C15orf23	cis	cerebellum	SCAN
rs2412511	PLA2G4E	cis	parietal	SCAN
rs2412511	JMJD7-PLA2G4B	cis	parietal	SCAN
rs2412511	CSNK1A1P1	cis	parietal	SCAN
rs2412511	C15orf23	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40617000-40622800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:40617200-40630200	Weak transcription	A549	lung
3	chr15:40617400-40621800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:40617400-40623000	Enhancers	Fetal Brain Male	brain
5	chr15:40617400-40623800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:40617400-40624000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:40617400-40626000	Weak transcription	Liver	Liver
8	chr15:40617400-40626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:40617400-40626400	Weak transcription	Pancreas	Pancrea
10	chr15:40617400-40627000	Weak transcription	Gastric	stomach
11	chr15:40617600-40622400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:40617600-40623400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr15:40617800-40623000	Enhancers	HMEC	breast
14	chr15:40617800-40625000	Weak transcription	Psoas Muscle	Psoas
15	chr15:40618000-40622600	Weak transcription	NHLF	lung
16	chr15:40618000-40624200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:40618000-40624400	Enhancers	NHDF-Ad	bronchial
18	chr15:40618000-40625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:40618000-40625800	Weak transcription	Dnd41	blood
20	chr15:40618200-40625800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:40618200-40626000	Weak transcription	Stomach Mucosa	stomach
22	chr15:40618400-40622200	Weak transcription	Brain Substantia Nigra	brain
23	chr15:40618400-40622400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:40618400-40622600	Genic enhancers	Osteobl	bone
25	chr15:40618400-40623000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:40618400-40624200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr15:40618400-40624400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr15:40618400-40624600	Weak transcription	Primary B cells from cord blood	blood
29	chr15:40618400-40625800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr15:40618400-40625800	Weak transcription	Esophagus	oesophagus
31	chr15:40618400-40626800	Weak transcription	Small Intestine	intestine
32	chr15:40618400-40628200	Weak transcription	Brain Germinal Matrix	brain
33	chr15:40618600-40623400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:40618800-40622600	Weak transcription	Colonic Mucosa	Colon
35	chr15:40618800-40623600	Enhancers	Brain Hippocampus Middle	brain
36	chr15:40619200-40621800	Weak transcription	Lung	lung
37	chr15:40619200-40623200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:40619400-40621800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:40619400-40622000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:40619400-40623400	Enhancers	Fetal Thymus	thymus
41	chr15:40619400-40623600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:40619400-40624200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:40619400-40624800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr15:40619400-40625400	Genic enhancers	Fetal Stomach	stomach
45	chr15:40619400-40627400	Enhancers	Placenta	Placenta
46	chr15:40619600-40621800	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr15:40619600-40623800	Enhancers	Fetal Lung	lung
48	chr15:40619600-40630400	Enhancers	Primary hematopoietic stem cells	blood
49	chr15:40619800-40621800	Weak transcription	Brain Angular Gyrus	brain
50	chr15:40619800-40621800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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