Variant report

Variant	rs62019866
Chromosome Location	chr15:40853923-40853924
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	chr15:40849898..40854344-chr15:40855565..40858408,6	K562	blood:

Variant related genes	Relation type
ENSG00000128891	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1051482	0.81[EUR][1000 genomes]
rs10851396	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11070279	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070280	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11852479	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11857247	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12148185	0.84[EUR][1000 genomes]
rs12899408	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12906755	0.83[EUR][1000 genomes]
rs12907448	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12907984	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12908114	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908443	0.84[EUR][1000 genomes]
rs12908867	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12914501	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915563	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12916323	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1453183	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17746659	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17747399	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2123534	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34303240	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34750756	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35884042	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36094699	0.80[EUR][1000 genomes]
rs3743146	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803353	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4457966	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55954396	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56384845	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61048252	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62018046	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62018048	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62018051	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62019883	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7162749	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164385	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7165054	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7181909	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72733469	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8025458	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028910	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8036938	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8038396	0.84[EUR][1000 genomes]
rs8042733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9806410	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs62019866	C15orf57	cis	Muscle Skeletal	GTEx
rs62019866	CCDC32	cis	multi-tissue	Pritchard
rs62019866	C15orf57	cis	Thyroid	GTEx
rs62019866	RP11-111A22.1	cis	Artery Tibial	GTEx
rs62019866	RP11-111A22.1	cis	Stomach	GTEx
rs62019866	C15orf57	cis	lung	GTEx
rs62019866	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs62019866	C15orf57	cis	Esophagus Mucosa	GTEx
rs62019866	C15orf57	cis	Esophagus Muscularis	GTEx
rs62019866	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs62019866	ZFYVE19	cis	multi-tissue	Pritchard
rs62019866	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs62019866	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs62019866	C15orf57	cis	Nerve Tibial	GTEx
rs62019866	C15orf57	cis	Artery Aorta	GTEx
rs62019866	RP11-111A22.1	cis	Artery Aorta	GTEx
rs62019866	C15orf57	cis	Artery Tibial	GTEx
rs62019866	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs62019866	C15orf57	cis	Adipose Subcutaneous	GTEx
rs62019866	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs62019866	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs62019866	RP11-111A22.1	cis	lung	GTEx
rs62019866	C15orf57	cis	Stomach	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
3	chr15:40828000-40856600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:40831600-40856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40838000-40856400	Weak transcription	A549	lung
6	chr15:40838600-40855600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:40840000-40856400	Weak transcription	Fetal Brain Female	brain
8	chr15:40840000-40856600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:40842400-40856200	Weak transcription	Colonic Mucosa	Colon
10	chr15:40843200-40856400	Weak transcription	Fetal Heart	heart
11	chr15:40843800-40856400	Weak transcription	HSMMtube	muscle
12	chr15:40846000-40855600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:40846200-40855000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:40846200-40856200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:40846600-40855000	Weak transcription	Psoas Muscle	Psoas
16	chr15:40846600-40855800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:40846600-40856400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:40846600-40856400	Weak transcription	Right Atrium	heart
19	chr15:40846600-40856600	Weak transcription	Aorta	Aorta
20	chr15:40846600-40856600	Weak transcription	Gastric	stomach
21	chr15:40846800-40856000	Weak transcription	Stomach Mucosa	stomach
22	chr15:40847200-40855000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:40847200-40855600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:40847200-40856400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:40847400-40855000	Weak transcription	Fetal Brain Male	brain
26	chr15:40847400-40856200	Weak transcription	Brain Germinal Matrix	brain
27	chr15:40847400-40856400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:40847400-40856600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:40848000-40854000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:40848000-40856400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:40848000-40856400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:40848000-40856400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:40848000-40856400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:40848400-40854400	Weak transcription	Hela-S3	cervix
35	chr15:40848400-40856400	Weak transcription	NHDF-Ad	bronchial
36	chr15:40848600-40854000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:40848600-40854000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:40848600-40854200	Weak transcription	Ovary	ovary
39	chr15:40848600-40854200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:40848600-40855000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:40848600-40855000	Weak transcription	Brain Anterior Caudate	brain
42	chr15:40848600-40855200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:40848600-40855800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:40848600-40856000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:40848600-40856200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr15:40848600-40856200	Weak transcription	HSMM	muscle
47	chr15:40848600-40856200	Weak transcription	HUVEC	blood vessel
48	chr15:40848600-40856200	Weak transcription	NHLF	lung
49	chr15:40848600-40856400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:40848600-40856400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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