Variant report

Variant	rs4886784
Chromosome Location	chr15:76524644-76524645
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76524104..76526710-chr15:76623821..76625694,2	K562	blood:
2	chr15:76515308..76517340-chr15:76524371..76526709,2	MCF-7	breast:
3	chr15:76515156..76518708-chr15:76522074..76525565,3	K562	blood:
4	chr15:76524058..76526377-chr15:76602062..76604868,2	MCF-7	breast:
5	chr15:76523878..76527250-chr15:76601184..76604398,3	K562	blood:
6	chr15:76524104..76527148-chr15:76623821..76625801,3	K562	blood:

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs11072576	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072577	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072578	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072579	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072583	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072585	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072587	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11629459	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11631690	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11631764	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11631874	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11633405	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11634060	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11634472	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634796	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11636278	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636851	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637473	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637855	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050813	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12050896	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12443449	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12595211	0.80[ASN][1000 genomes]
rs12916022	0.80[ASN][1000 genomes]
rs1474117	0.80[ASN][1000 genomes]
rs16968083	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1850722	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1875887	0.89[ASN][1000 genomes]
rs1875888	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2007928	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2016734	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404974	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2456049	0.91[ASN][1000 genomes]
rs2456050	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2456057	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2456071	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469210	0.80[ASN][1000 genomes]
rs2469548	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2938697	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34213321	0.81[ASN][1000 genomes]
rs35831705	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3898352	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3915459	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3915460	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3927264	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3958426	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3991792	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3991793	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3991794	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4592616	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886486	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4886487	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886488	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886777	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886779	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886780	0.86[AMR][1000 genomes]
rs4886781	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886783	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886787	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886789	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886791	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5012144	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55794488	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55805818	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56737606	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57182285	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60017340	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60290059	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60371615	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60561507	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61018254	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61275737	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61300240	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62027018	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62027047	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62027048	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62030232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62030245	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62030246	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6495197	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7177923	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179750	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7180462	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8028504	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8029637	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8030454	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8033494	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039063	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs870295	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs879625	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs883993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937732	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs937733	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959991	0.80[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4886784	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs4886784	SCAPER	cis	Whole Blood	GTEx
rs4886784	SCAPER	cis	Artery Tibial	GTEx
rs4886784	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4886784	SCAPER	cis	lung	GTEx
rs4886784	ISL2	cis	Whole Blood	GTEx
rs4886784	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs4886784	SCAPER	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76492800-76526400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr15:76493600-76526400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr15:76499200-76527400	Weak transcription	Fetal Brain Male	brain
4	chr15:76500600-76534800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:76503600-76551400	Weak transcription	Small Intestine	intestine
6	chr15:76506000-76526800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:76506200-76526800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:76506400-76525600	Weak transcription	Fetal Brain Female	brain
9	chr15:76507200-76551400	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:76508000-76525000	Weak transcription	NHLF	lung
11	chr15:76508000-76525400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:76508400-76546000	Weak transcription	Brain Anterior Caudate	brain
13	chr15:76508600-76525200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:76510000-76534600	Weak transcription	Brain Substantia Nigra	brain
15	chr15:76510200-76526000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:76510200-76555400	Weak transcription	Psoas Muscle	Psoas
17	chr15:76510400-76538000	Weak transcription	HUVEC	blood vessel
18	chr15:76510400-76538200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:76510400-76555000	Weak transcription	NH-A	brain
20	chr15:76511800-76525400	Strong transcription	Liver	Liver
21	chr15:76512000-76525400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:76512000-76525600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr15:76513200-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:76513400-76524800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:76513800-76551400	Weak transcription	Stomach Mucosa	stomach
26	chr15:76514200-76525000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr15:76514800-76525000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr15:76516400-76550600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:76517200-76551800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:76517400-76532600	Weak transcription	HSMM	muscle
31	chr15:76517400-76544600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:76517400-76549200	Weak transcription	Fetal Kidney	kidney
33	chr15:76517400-76550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:76517400-76550600	Weak transcription	Pancreas	Pancrea
35	chr15:76517400-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:76517600-76526000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:76517600-76526200	Weak transcription	Brain Germinal Matrix	brain
38	chr15:76517600-76526800	Weak transcription	Esophagus	oesophagus
39	chr15:76517600-76528000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:76517600-76528400	Weak transcription	Spleen	Spleen
41	chr15:76517600-76530400	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:76517600-76550600	Weak transcription	Aorta	Aorta
43	chr15:76517600-76550600	Weak transcription	Ovary	ovary
44	chr15:76517600-76551200	Weak transcription	Right Ventricle	heart
45	chr15:76517600-76551400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr15:76517600-76553800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr15:76518200-76525000	Weak transcription	Primary T cells from cord blood	blood
48	chr15:76518200-76532400	Weak transcription	A549	lung
49	chr15:76518200-76534600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:76518200-76534800	Weak transcription	Muscle Satellite Cultured Cells	--

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