Variant report

Variant	rs4592616
Chromosome Location	chr15:76550064-76550065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76548818..76551250-chr15:76556678..76559451,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11072576	0.88[EUR][1000 genomes]
rs11072577	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11072578	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11072579	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11072583	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072585	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072587	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11629459	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11631690	0.85[EUR][1000 genomes]
rs11631764	0.87[EUR][1000 genomes]
rs11631874	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11633405	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11634060	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11634472	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11634796	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11636278	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11636851	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11637855	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12050896	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12443449	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16968083	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1850722	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1875888	0.88[EUR][1000 genomes]
rs2007928	0.88[EUR][1000 genomes]
rs2016734	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2404974	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2456050	0.88[EUR][1000 genomes]
rs2456057	0.96[EUR][1000 genomes]
rs2456071	0.88[EUR][1000 genomes]
rs2469548	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2938697	0.81[EUR][1000 genomes]
rs35831705	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3784449	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3898352	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3915459	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3915460	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3927264	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3958426	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3991792	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3991793	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3991794	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886486	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886487	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886488	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886777	0.86[EUR][1000 genomes]
rs4886779	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4886780	0.83[AMR][1000 genomes]
rs4886781	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4886783	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886784	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886787	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886789	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886791	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5012144	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55805818	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56737606	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57182285	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60017340	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60290059	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60371615	0.88[EUR][1000 genomes]
rs60561507	0.83[EUR][1000 genomes]
rs61018254	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61275737	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61300240	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62027018	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62027047	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62027048	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62030232	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62030245	0.97[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62030246	0.82[EUR][1000 genomes]
rs6495197	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7177923	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7179750	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7180462	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8028504	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8029637	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8030454	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8033494	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8039063	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs870295	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs879625	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs883993	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs937732	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs937733	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv527608	chr15:76530267-76562738	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4592616	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4592616	SCAPER	cis	lung	GTEx
rs4592616	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs4592616	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs4592616	SCAPER	cis	Thyroid	GTEx
rs4592616	SCAPER	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76503600-76551400	Weak transcription	Small Intestine	intestine
2	chr15:76507200-76551400	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:76510200-76555400	Weak transcription	Psoas Muscle	Psoas
4	chr15:76510400-76555000	Weak transcription	NH-A	brain
5	chr15:76513200-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:76513800-76551400	Weak transcription	Stomach Mucosa	stomach
7	chr15:76516400-76550600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:76517200-76551800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:76517400-76550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:76517400-76550600	Weak transcription	Pancreas	Pancrea
11	chr15:76517400-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:76517600-76550600	Weak transcription	Aorta	Aorta
13	chr15:76517600-76550600	Weak transcription	Ovary	ovary
14	chr15:76517600-76551200	Weak transcription	Right Ventricle	heart
15	chr15:76517600-76551400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:76517600-76553800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:76518200-76550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:76521400-76551600	Weak transcription	Left Ventricle	heart
19	chr15:76522400-76554400	Weak transcription	Fetal Heart	heart
20	chr15:76523600-76550600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr15:76523600-76550600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:76523600-76550600	Weak transcription	Colonic Mucosa	Colon
23	chr15:76523600-76550600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:76523800-76551200	Weak transcription	Fetal Thymus	thymus
25	chr15:76523800-76551800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:76524000-76551600	Weak transcription	HMEC	breast
27	chr15:76524200-76553000	Weak transcription	NHDF-Ad	bronchial
28	chr15:76525200-76550600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:76525200-76550600	Weak transcription	GM12878-XiMat	blood
30	chr15:76527600-76550600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:76527600-76550600	Weak transcription	Esophagus	oesophagus
32	chr15:76529000-76550600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:76529000-76551000	Weak transcription	K562	blood
34	chr15:76530400-76550600	Weak transcription	Fetal Stomach	stomach
35	chr15:76531400-76551400	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:76532800-76551200	Weak transcription	HSMMtube	muscle
37	chr15:76533200-76550600	Weak transcription	HSMM	muscle
38	chr15:76535400-76550600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:76535400-76550600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:76535400-76550800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:76535400-76553000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr15:76535600-76550600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:76535600-76550600	Weak transcription	Adipose Nuclei	Adipose
44	chr15:76535600-76550600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:76535600-76550600	Weak transcription	Placenta	Placenta
46	chr15:76535600-76550600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr15:76535600-76550600	Weak transcription	Dnd41	blood
48	chr15:76535600-76550800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:76535600-76551200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:76535600-76551800	Weak transcription	Muscle Satellite Cultured Cells	--

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