Variant report

Variant	rs62019879
Chromosome Location	chr15:40877516-40877517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40875697..40878218-chr15:40879677..40882700,3	K562	blood:
2	chr15:40875804..40877878-chr15:41405943..41408049,2	K562	blood:
3	chr15:40876093..40878968-chr15:40880473..40883736,4	K562	blood:
4	chr15:40871337..40873868-chr15:40877002..40878740,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 19 )

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

rs_ID	r²[population]
rs10152546	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1044474	0.90[EUR][1000 genomes]
rs10518697	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1058734	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070283	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11630273	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11633184	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637245	0.92[EUR][1000 genomes]
rs11637422	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12324748	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12385982	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12441754	0.85[EUR][1000 genomes]
rs12903817	0.90[EUR][1000 genomes]
rs12907442	0.83[EUR][1000 genomes]
rs12908316	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12913296	0.93[EUR][1000 genomes]
rs12913739	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915171	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12915636	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13329076	0.89[EUR][1000 genomes]
rs17673703	0.93[EUR][1000 genomes]
rs17674454	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17747423	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17747633	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1814541	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1814542	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412525	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28529389	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28634695	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28647196	0.84[EUR][1000 genomes]
rs28669075	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34739056	0.85[EUR][1000 genomes]
rs34824658	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35127391	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35684277	0.89[EUR][1000 genomes]
rs35842610	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4923880	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924486	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62019876	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71471880	0.89[EUR][1000 genomes]
rs7165509	0.89[EUR][1000 genomes]
rs7170288	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7175747	0.88[EUR][1000 genomes]
rs8029530	0.85[EUR][1000 genomes]
rs8036891	0.85[EUR][1000 genomes]
rs8037180	0.87[EUR][1000 genomes]
rs8038122	0.89[EUR][1000 genomes]
rs8042386	0.87[EUR][1000 genomes]
rs9920642	0.89[EUR][1000 genomes]
rs9920676	0.87[AMR][1000 genomes];0.95[EUR][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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs62019879	C15orf57	cis	Heart Left Ventricle	GTEx
rs62019879	RP11-111A22.1	cis	Artery Tibial	GTEx
rs62019879	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs62019879	C15orf57	cis	Esophagus Mucosa	GTEx
rs62019879	C15orf57	cis	Stomach	GTEx
rs62019879	RP11-111A22.1	cis	Artery Aorta	GTEx
rs62019879	C15orf57	cis	lung	GTEx
rs62019879	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs62019879	C15orf57	cis	Muscle Skeletal	GTEx
rs62019879	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs62019879	RP11-111A22.1	cis	Stomach	GTEx
rs62019879	C15orf57	cis	Nerve Tibial	GTEx
rs62019879	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs62019879	C15orf57	cis	Adipose Subcutaneous	GTEx
rs62019879	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs62019879	C15orf57	cis	Artery Tibial	GTEx
rs62019879	C15orf57	cis	Esophagus Muscularis	GTEx
rs62019879	C15orf57	cis	Artery Aorta	GTEx
rs62019879	RP11-111A22.1	cis	lung	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40866400-40878200	Weak transcription	Brain Angular Gyrus	brain
2	chr15:40866600-40881800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr15:40866600-40881800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:40866600-40881800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:40867400-40883600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:40875400-40881600	Weak transcription	Brain Anterior Caudate	brain
7	chr15:40875400-40881800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:40875400-40882000	Weak transcription	Primary B cells from cord blood	blood
9	chr15:40875600-40881800	Weak transcription	Brain Substantia Nigra	brain
10	chr15:40875600-40882200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr15:40875600-40882200	Weak transcription	Fetal Intestine Small	intestine
12	chr15:40875600-40882200	Weak transcription	Right Atrium	heart
13	chr15:40876600-40882200	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:40876800-40881800	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:40876800-40881800	Weak transcription	K562	blood
16	chr15:40877000-40881600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:40877200-40877600	Enhancers	HepG2	liver
18	chr15:40877200-40881600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:40877200-40881800	Weak transcription	Hela-S3	cervix
20	chr15:40877200-40882200	Weak transcription	Liver	Liver

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