Variant report

Variant	rs1824083
Chromosome Location	chr15:52061124-52061125
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52041772..52043796-chr15:52059873..52062736,2	MCF-7	breast:
2	chr15:52058591..52061806-chr15:52062033..52065705,3	K562	blood:
3	chr15:52049744..52051270-chr15:52058518..52061301,2	K562	blood:
4	chr15:52043955..52045654-chr15:52058986..52062034,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction
ENSG00000259377	Chromatin interaction
ENSG00000128872	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1867985	0.86[YRI][hapmap]
rs2162224	0.83[YRI][hapmap]
rs2436663	0.80[YRI][hapmap]
rs2436664	0.80[YRI][hapmap]
rs2554319	0.80[YRI][hapmap]
rs2554329	0.82[YRI][hapmap]
rs2554331	0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2554333	0.80[YRI][hapmap]
rs2554346	0.86[YRI][hapmap]
rs2554356	0.80[YRI][hapmap]
rs2554357	0.86[YRI][hapmap]
rs2570244	0.80[YRI][hapmap]
rs2570245	0.80[YRI][hapmap]
rs2570246	0.80[YRI][hapmap]
rs2570256	0.80[YRI][hapmap]
rs2570257	0.80[YRI][hapmap]
rs2570267	0.80[YRI][hapmap]
rs2570270	0.86[YRI][hapmap]
rs2570272	0.86[YRI][hapmap]
rs2593171	0.80[YRI][hapmap]
rs2593175	0.80[YRI][hapmap]
rs2593186	0.86[YRI][hapmap]
rs2623246	0.80[YRI][hapmap]
rs2623269	0.80[YRI][hapmap]
rs2623274	0.80[YRI][hapmap]
rs2623277	0.80[YRI][hapmap]
rs2623290	0.83[YRI][hapmap]
rs2652596	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs543024	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	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	esv3411789	chr15:52052789-52087519	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52051200-52077600	Weak transcription	Psoas Muscle	Psoas
2	chr15:52051400-52061200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr15:52051400-52068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:52051400-52068400	Weak transcription	Stomach Mucosa	stomach
5	chr15:52052200-52061200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:52052200-52064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:52052200-52068200	Weak transcription	Fetal Intestine Small	intestine
8	chr15:52052200-52068600	Weak transcription	HMEC	breast
9	chr15:52052200-52074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:52052200-52076000	Weak transcription	Fetal Brain Male	brain
11	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
12	chr15:52052400-52067000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:52052400-52068200	Weak transcription	Fetal Intestine Large	intestine
14	chr15:52052400-52073200	Weak transcription	NHDF-Ad	bronchial
15	chr15:52052400-52078400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:52052600-52065200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:52052600-52106600	Weak transcription	HSMM	muscle
18	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
19	chr15:52058400-52061400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:52058400-52064200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:52058400-52067600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:52058600-52068200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:52058800-52072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:52060000-52061200	Enhancers	Spleen	Spleen
25	chr15:52060000-52061600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:52060000-52061600	Strong transcription	NHLF	lung
27	chr15:52060000-52061800	Strong transcription	Esophagus	oesophagus
28	chr15:52060000-52061800	Strong transcription	Dnd41	blood
29	chr15:52060000-52062600	Strong transcription	Fetal Brain Female	brain
30	chr15:52060000-52063000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:52060000-52063000	Strong transcription	Fetal Stomach	stomach
32	chr15:52060000-52063200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:52060000-52063600	Strong transcription	Ovary	ovary
34	chr15:52060200-52061400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:52060200-52061800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:52060200-52062400	Strong transcription	Brain Hippocampus Middle	brain
37	chr15:52060200-52062600	Strong transcription	Aorta	Aorta
38	chr15:52060200-52062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:52060200-52068200	Weak transcription	Liver	Liver
40	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr15:52060400-52061200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr15:52060400-52061200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:52060400-52061800	Strong transcription	Pancreatic Islets	Pancreatic Islet
44	chr15:52060400-52062200	Strong transcription	Brain Cingulate Gyrus	brain
45	chr15:52060400-52062400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:52060400-52062400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:52060400-52063600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:52060400-52064600	Strong transcription	Fetal Muscle Leg	muscle
49	chr15:52060400-52068400	Strong transcription	Thymus	Thymus
50	chr15:52060400-52069200	Weak transcription	Placenta	Placenta

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