Variant report

Variant	rs3991794
Chromosome Location	chr15:76591820-76591821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76585221..76587431-chr15:76590533..76592803,2	K562	blood:
2	chr15:76591467..76593995-chr15:76626637..76628156,2	K562	blood:
3	chr15:76591677..76593698-chr15:76599453..76601197,2	MCF-7	breast:
4	chr15:76582923..76594852-chr15:76601949..76606997,18	MCF-7	breast:
5	chr15:76591467..76593414-chr15:76626364..76628156,2	K562	blood:
6	chr15:76584135..76596152-chr15:76600630..76606670,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs11072576	0.84[EUR][1000 genomes]
rs11072577	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072578	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072579	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072583	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072585	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072587	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11629459	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11631764	0.81[EUR][1000 genomes]
rs11631874	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11633405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634060	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634472	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11634796	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636851	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637855	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12050896	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.99[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];1.00[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	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2007928	0.84[EUR][1000 genomes]
rs2016734	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2056251	0.90[ASN][1000 genomes]
rs2404974	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2456050	0.84[EUR][1000 genomes]
rs2456057	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2456071	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2469210	0.99[ASN][1000 genomes]
rs2469548	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2938697	0.84[AMR][1000 genomes];0.89[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	0.89[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915460	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3991792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3991793	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];0.99[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886777	0.82[EUR][1000 genomes]
rs4886779	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886781	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886783	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886784	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886787	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886789	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886791	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012144	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55794488	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55805818	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56372945	0.81[AFR][1000 genomes]
rs56737606	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.84[EUR][1000 genomes]
rs60290059	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60371615	0.84[EUR][1000 genomes]
rs60561507	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61018254	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61275737	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61300240	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62027018	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62027047	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62027048	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62027051	0.85[AFR][1000 genomes]
rs62030232	0.89[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];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6495197	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7177923	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7179750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8028504	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029637	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033494	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8039063	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs870295	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs879625	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs883993	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs937732	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs937733	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3991794	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs3991794	ISL2	cis	Whole Blood	GTEx
rs3991794	SCAPER	cis	lung	GTEx
rs3991794	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs3991794	SCAPER	cis	Whole Blood	GTEx
rs3991794	SCAPER	cis	Thyroid	GTEx
rs3991794	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs3991794	SCAPER	cis	Artery Tibial	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76556800-76594600	Weak transcription	Esophagus	oesophagus
2	chr15:76558000-76603000	Weak transcription	Aorta	Aorta
3	chr15:76573200-76592200	Weak transcription	Fetal Kidney	kidney
4	chr15:76573200-76593200	Weak transcription	Right Ventricle	heart
5	chr15:76574800-76601400	Weak transcription	Pancreas	Pancrea
6	chr15:76574800-76602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:76576200-76602800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:76579200-76602000	Weak transcription	Thymus	Thymus
9	chr15:76579400-76592600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:76579400-76592800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:76579600-76592000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:76579600-76592600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:76579600-76592600	Weak transcription	Dnd41	blood
14	chr15:76579600-76602000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:76579800-76593000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:76580200-76596000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr15:76580400-76593200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr15:76580600-76600400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:76582400-76594400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:76583400-76592000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:76583400-76592600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:76583600-76602000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:76583800-76602000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:76584000-76601400	Weak transcription	Placenta	Placenta
25	chr15:76584600-76602400	Weak transcription	Primary B cells from cord blood	blood
26	chr15:76584800-76602000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr15:76584800-76602200	Weak transcription	Fetal Thymus	thymus
28	chr15:76585000-76602000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:76585200-76602400	Weak transcription	Primary T cells from cord blood	blood
30	chr15:76586200-76602000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:76586200-76602400	Weak transcription	NH-A	brain
32	chr15:76586400-76597600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:76586400-76601800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:76586400-76602000	Weak transcription	Stomach Mucosa	stomach
35	chr15:76586400-76602400	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:76586600-76592000	Weak transcription	K562	blood
37	chr15:76586800-76594200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:76588000-76602000	Weak transcription	Psoas Muscle	Psoas
39	chr15:76589600-76602000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:76590200-76592000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:76590600-76592400	Enhancers	A549	lung
42	chr15:76590600-76592800	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr15:76590800-76593400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr15:76590800-76600600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:76591000-76593000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:76591000-76593200	Weak transcription	Hela-S3	cervix
47	chr15:76591000-76593400	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr15:76591000-76602000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:76591000-76602000	Weak transcription	Ovary	ovary
50	chr15:76591400-76592200	Enhancers	Primary neutrophils fromperipheralblood	blood

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