Variant report

Variant	rs4886781
Chromosome Location	chr15:76507952-76507953
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	chr15:76503018..76504936-chr15:76506682..76510491,3	MCF-7	breast:
2	chr15:76507862..76509861-chr15:76511366..76512981,2	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11072576	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072577	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072578	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072579	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072583	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072585	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072587	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11629459	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11631690	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11631764	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11631874	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11633405	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11634060	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11634472	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11634796	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11636278	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11636851	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11637473	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11637855	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12050813	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12050896	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12443449	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12595211	0.81[ASN][1000 genomes]
rs12916022	0.81[ASN][1000 genomes]
rs1474117	0.81[ASN][1000 genomes]
rs16968083	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1850722	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1875887	0.90[ASN][1000 genomes]
rs1875888	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2007928	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2016734	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404974	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2456049	0.92[ASN][1000 genomes]
rs2456050	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456057	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2456071	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2469548	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2938697	0.89[ASN][1000 genomes]
rs34213321	0.82[ASN][1000 genomes]
rs35831705	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784449	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3898352	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3915459	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3915460	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3927264	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3958426	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3991792	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3991793	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3991794	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4592616	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4886484	0.80[ASN][1000 genomes]
rs4886485	0.81[ASN][1000 genomes]
rs4886486	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886487	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886488	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886777	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886779	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886780	0.90[AMR][1000 genomes]
rs4886783	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886784	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886787	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886789	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886791	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5012144	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55794488	0.81[AMR][1000 genomes]
rs55805818	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56737606	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57182285	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60017340	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60290059	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60371615	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60561507	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61018254	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61275737	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61300240	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62027018	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62027047	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62027048	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62030229	0.81[AMR][1000 genomes]
rs62030232	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62030245	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62030246	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6495197	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7177923	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7179750	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7180462	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8028504	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8029637	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8030454	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8033494	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8039063	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs869452	0.81[ASN][1000 genomes]
rs870295	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879625	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883993	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs937732	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs937733	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959991	0.81[ASN][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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4886781	SCAPER	cis	lung	GTEx
rs4886781	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4886781	SCAPER	cis	Thyroid	GTEx
rs4886781	SCAPER	cis	Whole Blood	GTEx
rs4886781	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs4886781	SCAPER	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76486800-76516600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr15:76489400-76519800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:76492000-76509600	Weak transcription	K562	blood
4	chr15:76492400-76510000	Strong transcription	Placenta	Placenta
5	chr15:76492800-76517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:76492800-76526400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:76493600-76526400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:76494600-76510400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:76495400-76510400	Strong transcription	Adipose Nuclei	Adipose
10	chr15:76495800-76508600	Strong transcription	A549	lung
11	chr15:76496200-76510400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:76497000-76518200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr15:76497400-76509400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:76498200-76508800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr15:76498200-76509200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:76498200-76510200	Strong transcription	Fetal Intestine Large	intestine
17	chr15:76498200-76511000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:76498200-76511600	Strong transcription	Primary T cells from cord blood	blood
19	chr15:76498400-76510600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:76498600-76510400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr15:76499200-76509000	Weak transcription	Stomach Mucosa	stomach
22	chr15:76499200-76509400	Weak transcription	Brain Germinal Matrix	brain
23	chr15:76499200-76509600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:76499200-76516800	Weak transcription	Brain Angular Gyrus	brain
25	chr15:76499200-76527400	Weak transcription	Fetal Brain Male	brain
26	chr15:76499800-76508200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:76499800-76509000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:76500000-76510400	Strong transcription	Liver	Liver
29	chr15:76500000-76510400	Strong transcription	Spleen	Spleen
30	chr15:76500200-76508400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr15:76500200-76508400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr15:76500200-76510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:76500400-76510400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr15:76500600-76508200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:76500600-76508200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:76500600-76509600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:76500600-76534800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:76500800-76508400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:76500800-76510400	Strong transcription	Fetal Intestine Small	intestine
40	chr15:76501000-76508400	Strong transcription	Lung	lung
41	chr15:76501000-76510400	Strong transcription	Fetal Muscle Leg	muscle
42	chr15:76501200-76508600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr15:76501200-76509600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:76501200-76524200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:76501400-76508200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:76501600-76508200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:76501600-76509200	Strong transcription	Dnd41	blood
48	chr15:76501600-76510400	Strong transcription	Primary B cells from cord blood	blood
49	chr15:76501600-76510400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr15:76501600-76512400	Strong transcription	HepG2	liver

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