Variant report

Variant	rs17746659
Chromosome Location	chr15:40859951-40859952
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1051482	0.84[EUR][1000 genomes]
rs10851396	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11070279	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070280	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852479	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11855517	0.82[EUR][1000 genomes]
rs11857247	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148185	0.87[EUR][1000 genomes]
rs12899408	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906755	0.86[EUR][1000 genomes]
rs12907448	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12907984	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12908114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908443	0.88[EUR][1000 genomes]
rs12908867	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12914501	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915563	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12916323	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1453183	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17747399	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2123534	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28798094	0.82[EUR][1000 genomes]
rs34303240	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34750756	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35884042	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36094699	0.82[EUR][1000 genomes]
rs3743146	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803353	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4457966	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55954396	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56384845	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61048252	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62018046	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62018048	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62018051	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62019866	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62019883	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62019934	0.81[EUR][1000 genomes]
rs7162749	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7164385	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181909	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72733469	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs731640	0.80[EUR][1000 genomes]
rs8025458	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8028910	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8036938	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8038396	0.87[EUR][1000 genomes]
rs8042733	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806410	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs17746659	C15orf57	cis	Muscle Skeletal	GTEx
rs17746659	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs17746659	C15orf57	cis	Esophagus Muscularis	GTEx
rs17746659	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs17746659	RP11-111A22.1	cis	Artery Aorta	GTEx
rs17746659	ZFYVE19	cis	multi-tissue	Pritchard
rs17746659	CCDC32	cis	multi-tissue	Pritchard
rs17746659	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs17746659	C15orf57	cis	Artery Aorta	GTEx
rs17746659	RP11-111A22.1	cis	lung	GTEx
rs17746659	C15orf57	cis	Esophagus Mucosa	GTEx
rs17746659	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs17746659	C15orf57	cis	Artery Tibial	GTEx
rs17746659	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs17746659	C15orf57	cis	lung	GTEx
rs17746659	C15orf57	cis	Adipose Subcutaneous	GTEx
rs17746659	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs17746659	C15orf57	cis	Stomach	GTEx
rs17746659	C15orf57	cis	Nerve Tibial	GTEx
rs17746659	RP11-111A22.1	cis	Artery Tibial	GTEx
rs17746659	RP11-111A22.1	cis	Stomach	GTEx
rs17746659	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40857200-40861200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:40857400-40860800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:40857600-40860800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:40857800-40860600	Weak transcription	Brain Angular Gyrus	brain
5	chr15:40857800-40860800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:40857800-40860800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:40857800-40860800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:40857800-40860800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:40857800-40860800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:40857800-40860800	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:40857800-40860800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:40857800-40860800	Weak transcription	Fetal Lung	lung
13	chr15:40857800-40860800	Weak transcription	Stomach Mucosa	stomach
14	chr15:40857800-40860800	Weak transcription	NHLF	lung
15	chr15:40857800-40860800	Weak transcription	Osteobl	bone
16	chr15:40857800-40861000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:40857800-40861000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:40857800-40861000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:40857800-40861000	Weak transcription	HSMM	muscle
20	chr15:40857800-40861000	Weak transcription	HSMMtube	muscle
21	chr15:40857800-40861200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:40857800-40861200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:40858000-40860000	Enhancers	K562	blood
24	chr15:40858000-40860600	Weak transcription	Primary T cells from cord blood	blood
25	chr15:40858000-40860600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:40858000-40860600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr15:40858000-40860600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:40858000-40860600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr15:40858000-40860600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:40858000-40860600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:40858000-40860600	Weak transcription	Brain Anterior Caudate	brain
32	chr15:40858000-40860600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:40858000-40860600	Weak transcription	Brain Germinal Matrix	brain
34	chr15:40858000-40860600	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:40858000-40860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:40858000-40860600	Weak transcription	Fetal Muscle Leg	muscle
37	chr15:40858000-40860600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:40858000-40860600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:40858000-40860600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:40858000-40860600	Weak transcription	A549	lung
41	chr15:40858000-40860600	Weak transcription	GM12878-XiMat	blood
42	chr15:40858000-40860800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:40858000-40860800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:40858000-40860800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:40858000-40860800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:40858000-40860800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr15:40858000-40860800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr15:40858000-40860800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:40858000-40860800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:40858000-40860800	Weak transcription	Adipose Nuclei	Adipose

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