Variant report

Variant	rs62027048
Chromosome Location	chr15:76595539-76595540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76544452..76546096-chr15:76594842..76597677,2	K562	blood:
2	chr15:76592629..76596591-chr15:76598250..76600495,3	MCF-7	breast:
3	chr15:76584135..76596152-chr15:76600630..76606670,15	MCF-7	breast:
4	chr15:76595069..76597858-chr15:76601766..76604708,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11072576	0.83[EUR][1000 genomes]
rs11072577	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072578	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072579	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072583	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072585	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072587	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11629459	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11631874	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11633405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634060	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634472	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11634796	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636278	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636851	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637855	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12050896	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439484	0.80[ASN][1000 genomes]
rs12443449	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907668	0.81[ASN][1000 genomes]
rs12908334	0.80[ASN][1000 genomes]
rs12911035	0.80[ASN][1000 genomes]
rs16968083	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17361504	0.82[ASN][1000 genomes]
rs1850722	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1875888	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2007928	0.83[EUR][1000 genomes]
rs2016734	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2056251	0.90[ASN][1000 genomes]
rs2404974	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2456050	0.83[EUR][1000 genomes]
rs2456057	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2456071	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2469210	0.99[ASN][1000 genomes]
rs2469548	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2938697	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35831705	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3759853	0.82[ASN][1000 genomes]
rs3784449	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3898352	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3915459	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915460	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3927264	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3958426	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3991792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3991793	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3991794	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4381566	0.81[ASN][1000 genomes]
rs4592616	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886486	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886487	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886488	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886777	0.81[EUR][1000 genomes]
rs4886779	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886781	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886783	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886784	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886787	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886789	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886791	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012144	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55794488	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55805818	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56737606	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57182285	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60017340	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60290059	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60371615	0.83[EUR][1000 genomes]
rs60561507	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61018254	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61275737	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61300240	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62027018	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62027047	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62027051	0.83[AFR][1000 genomes]
rs62030232	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62030245	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62030246	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6495197	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7177923	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7179750	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8028504	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029637	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030454	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033494	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8039063	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs870295	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs879625	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs883993	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs937732	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs937733	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62027048	SCAPER	cis	Thyroid	GTEx
rs62027048	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs62027048	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs62027048	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs62027048	SCAPER	cis	Artery Tibial	GTEx
rs62027048	SCAPER	cis	lung	GTEx
rs62027048	ISL2	cis	Whole Blood	GTEx
rs62027048	SCAPER	cis	Whole Blood	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76558000-76603000	Weak transcription	Aorta	Aorta
2	chr15:76574800-76601400	Weak transcription	Pancreas	Pancrea
3	chr15:76574800-76602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:76576200-76602800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:76579200-76602000	Weak transcription	Thymus	Thymus
6	chr15:76579600-76602000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:76580200-76596000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:76580600-76600400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:76583600-76602000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:76583800-76602000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:76584000-76601400	Weak transcription	Placenta	Placenta
12	chr15:76584600-76602400	Weak transcription	Primary B cells from cord blood	blood
13	chr15:76584800-76602000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:76584800-76602200	Weak transcription	Fetal Thymus	thymus
15	chr15:76585000-76602000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:76585200-76602400	Weak transcription	Primary T cells from cord blood	blood
17	chr15:76586200-76602000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:76586200-76602400	Weak transcription	NH-A	brain
19	chr15:76586400-76597600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:76586400-76601800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:76586400-76602000	Weak transcription	Stomach Mucosa	stomach
22	chr15:76586400-76602400	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:76588000-76602000	Weak transcription	Psoas Muscle	Psoas
24	chr15:76589600-76602000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:76590800-76600600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:76591000-76602000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:76591000-76602000	Weak transcription	Ovary	ovary
28	chr15:76591600-76601800	Weak transcription	NHEK	skin
29	chr15:76591800-76596400	Weak transcription	Fetal Intestine Small	intestine
30	chr15:76591800-76600600	Weak transcription	HMEC	breast
31	chr15:76592000-76599800	Weak transcription	Left Ventricle	heart
32	chr15:76592000-76600400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:76592000-76600800	Weak transcription	Gastric	stomach
34	chr15:76592000-76602000	Weak transcription	Fetal Intestine Large	intestine
35	chr15:76592000-76602200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr15:76592000-76602200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:76592200-76599200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:76592200-76601400	Weak transcription	Right Atrium	heart
39	chr15:76592200-76602200	Weak transcription	Spleen	Spleen
40	chr15:76592400-76598000	Weak transcription	A549	lung
41	chr15:76592400-76602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:76592600-76602400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr15:76593000-76600800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:76593000-76601800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr15:76593200-76596400	Weak transcription	GM12878-XiMat	blood
46	chr15:76593200-76602000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:76593200-76602000	Weak transcription	Small Intestine	intestine
48	chr15:76593400-76597800	Weak transcription	HepG2	liver
49	chr15:76593400-76599800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:76593400-76600600	Weak transcription	K562	blood

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