Variant report

Variant	rs4886488
Chromosome Location	chr15:76596700-76596701
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	chr15:76544452..76546096-chr15:76594842..76597677,2	K562	blood:
2	chr15:76595069..76597858-chr15:76601766..76604708,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs11072576	0.80[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs11072577	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072578	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072579	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072580	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs11072583	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072585	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072587	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072591	0.82[JPT][hapmap]
rs11072597	0.82[JPT][hapmap]
rs11072598	0.87[JPT][hapmap]
rs11629459	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11629888	0.82[JPT][hapmap]
rs11631874	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11633405	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634019	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs11634060	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634472	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11634796	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11635463	0.82[JPT][hapmap]
rs11636278	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636851	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637855	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11638767	0.88[JPT][hapmap]
rs11857015	0.83[JPT][hapmap]
rs11857327	0.88[JPT][hapmap]
rs12050896	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439484	0.89[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs12442266	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs12443449	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591100	0.82[JPT][hapmap]
rs12592501	0.89[CHB][hapmap]
rs12595211	0.89[CHB][hapmap]
rs12595717	0.83[CHB][hapmap]
rs12898415	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs12901160	0.84[CHB][hapmap]
rs12902506	0.89[CHB][hapmap]
rs12906143	0.80[JPT][hapmap]
rs12907668	0.89[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12908334	0.89[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs12909656	0.82[JPT][hapmap]
rs12909718	0.89[CHB][hapmap]
rs12911035	0.80[ASN][1000 genomes]
rs12913096	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1474117	0.89[CHB][hapmap]
rs157783	0.82[JPT][hapmap]
rs1607015	0.81[CEU][hapmap]
rs1607017	0.81[JPT][hapmap]
rs16968083	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17361504	0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs1850722	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1875888	0.84[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2007928	0.83[EUR][1000 genomes]
rs2016734	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2056251	0.90[ASN][1000 genomes]
rs2139190	0.88[CHB][hapmap]
rs2176623	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2280306	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs2404974	0.86[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2456046	0.89[CHB][hapmap]
rs2456050	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2456057	0.89[EUR][1000 genomes]
rs2456071	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2469210	0.99[ASN][1000 genomes]
rs2469249	0.82[JPT][hapmap]
rs2469541	0.89[CHB][hapmap]
rs2469542	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2469548	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2469565	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs283789	0.81[JPT][hapmap]
rs283793	0.81[JPT][hapmap]
rs283795	0.81[JPT][hapmap]
rs2938697	0.88[EUR][1000 genomes]
rs2957614	0.82[JPT][hapmap]
rs2959850	0.94[CHB][hapmap]
rs2959853	0.89[CHB][hapmap]
rs35831705	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3759853	0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs3765115	0.82[JPT][hapmap]
rs3784449	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3866543	0.82[JPT][hapmap]
rs3898352	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3915459	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915460	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3927264	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3958426	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3991792	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3991793	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3991794	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437131	0.81[JPT][hapmap]
rs4381566	0.81[ASN][1000 genomes]
rs4592616	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886484	0.89[CHB][hapmap]
rs4886485	0.84[CHB][hapmap]
rs4886486	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886487	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886493	0.82[JPT][hapmap]
rs4886495	0.82[JPT][hapmap]
rs4886777	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4886779	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886780	0.81[AMR][1000 genomes]
rs4886781	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886783	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886784	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886787	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886788	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4886789	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886791	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886798	0.82[JPT][hapmap]
rs4886800	0.83[JPT][hapmap]
rs4886805	0.82[JPT][hapmap]
rs5012144	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55794488	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55805818	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56737606	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57182285	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60017340	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60290059	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60371615	0.83[EUR][1000 genomes]
rs60561507	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61018254	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61275737	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61300240	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62027018	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62027047	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62027048	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62030232	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62030245	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62030246	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6495197	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7174889	0.89[CHB][hapmap]
rs7177370	0.84[YRI][hapmap]
rs7177923	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7179750	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180462	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs744336	0.82[JPT][hapmap]
rs8028504	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029637	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030454	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033494	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8039063	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs869452	0.89[CHB][hapmap]
rs870295	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs879625	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs883993	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs908817	0.82[JPT][hapmap]
rs937732	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs937733	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs959991	0.89[CHB][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4886488	SCAPER	cis	Thyroid	GTEx
rs4886488	SCAPER	cis	lung	GTEx
rs4886488	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs4886488	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs4886488	SCAPER	cis	Whole Blood	GTEx
rs4886488	SCAPER	cis	Artery Tibial	GTEx
rs4886488	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	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	chr15:76580600-76600400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:76583600-76602000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:76583800-76602000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:76584000-76601400	Weak transcription	Placenta	Placenta
11	chr15:76584600-76602400	Weak transcription	Primary B cells from cord blood	blood
12	chr15:76584800-76602000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:76584800-76602200	Weak transcription	Fetal Thymus	thymus
14	chr15:76585000-76602000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:76585200-76602400	Weak transcription	Primary T cells from cord blood	blood
16	chr15:76586200-76602000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:76586200-76602400	Weak transcription	NH-A	brain
18	chr15:76586400-76597600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:76586400-76601800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:76586400-76602000	Weak transcription	Stomach Mucosa	stomach
21	chr15:76586400-76602400	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:76588000-76602000	Weak transcription	Psoas Muscle	Psoas
23	chr15:76589600-76602000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:76590800-76600600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:76591000-76602000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:76591000-76602000	Weak transcription	Ovary	ovary
27	chr15:76591600-76601800	Weak transcription	NHEK	skin
28	chr15:76591800-76600600	Weak transcription	HMEC	breast
29	chr15:76592000-76599800	Weak transcription	Left Ventricle	heart
30	chr15:76592000-76600400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:76592000-76600800	Weak transcription	Gastric	stomach
32	chr15:76592000-76602000	Weak transcription	Fetal Intestine Large	intestine
33	chr15:76592000-76602200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr15:76592000-76602200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:76592200-76599200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:76592200-76601400	Weak transcription	Right Atrium	heart
37	chr15:76592200-76602200	Weak transcription	Spleen	Spleen
38	chr15:76592400-76598000	Weak transcription	A549	lung
39	chr15:76592400-76602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:76592600-76602400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:76593000-76600800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:76593000-76601800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr15:76593200-76602000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:76593200-76602000	Weak transcription	Small Intestine	intestine
45	chr15:76593400-76597800	Weak transcription	HepG2	liver
46	chr15:76593400-76599800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:76593400-76600600	Weak transcription	K562	blood
48	chr15:76593400-76602000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr15:76593400-76602000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:76593400-76602400	Weak transcription	Lung	lung

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