Variant report

Variant	rs4923880
Chromosome Location	chr15:40925936-40925937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10152546	0.88[EUR][1000 genomes]
rs1044474	0.85[EUR][1000 genomes]
rs10518697	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1058734	0.89[EUR][1000 genomes]
rs11070283	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11630273	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11633184	0.91[EUR][1000 genomes]
rs11637245	0.88[EUR][1000 genomes]
rs11637422	0.90[EUR][1000 genomes]
rs12148915	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12324748	0.91[EUR][1000 genomes]
rs12385982	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12441754	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12442560	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12591044	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12592524	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12903817	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907442	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908316	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12913296	0.88[EUR][1000 genomes]
rs12913739	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12915171	0.88[EUR][1000 genomes]
rs12915636	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13329076	0.83[EUR][1000 genomes]
rs17673703	0.88[EUR][1000 genomes]
rs17674454	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17747423	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17747633	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1801321	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1814541	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2412525	0.91[EUR][1000 genomes]
rs2619682	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28529389	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28634695	0.88[EUR][1000 genomes]
rs28647196	0.81[EUR][1000 genomes]
rs28669075	0.88[EUR][1000 genomes]
rs28866515	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28891195	0.85[AMR][1000 genomes]
rs34305357	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34739056	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34824658	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35127391	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35684277	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35842610	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924492	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4924496	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4924502	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5030789	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59244061	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62019876	0.91[EUR][1000 genomes]
rs62019879	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71471880	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165509	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7170288	0.90[EUR][1000 genomes]
rs7175747	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176245	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7176590	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7177265	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7180135	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7182499	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8029530	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036891	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8037180	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8038122	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8042386	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs957603	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9920642	0.90[EUR][1000 genomes]
rs9920676	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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	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
2	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
3	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
4	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs4923880	RP11-111A22.1	cis	lung	GTEx
rs4923880	C15orf57	cis	Esophagus Mucosa	GTEx
rs4923880	C15orf57	cis	lung	GTEx
rs4923880	C15orf57	cis	Heart Left Ventricle	GTEx
rs4923880	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs4923880	RAD51	cis	multi-tissue	Pritchard
rs4923880	CCDC32	cis	multi-tissue	Pritchard
rs4923880	C15orf57	cis	Muscle Skeletal	GTEx
rs4923880	RP11-111A22.1	cis	Artery Tibial	GTEx
rs4923880	C15orf57	cis	Stomach	GTEx
rs4923880	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs4923880	C15orf57	cis	Adipose Subcutaneous	GTEx
rs4923880	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs4923880	C15orf57	cis	Esophagus Muscularis	GTEx
rs4923880	C15orf57	cis	Nerve Tibial	GTEx
rs4923880	RP11-111A22.1	cis	Artery Aorta	GTEx
rs4923880	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs4923880	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs4923880	C15orf57	cis	Artery Aorta	GTEx
rs4923880	C15orf57	cis	Artery Tibial	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887600-40941800	Weak transcription	Fetal Intestine Large	intestine
2	chr15:40887800-40933200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
4	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:40900000-40943600	Weak transcription	NH-A	brain
10	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
11	chr15:40903600-40927800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
15	chr15:40904800-40927800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:40906400-40930200	Strong transcription	Dnd41	blood
17	chr15:40911400-40930600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:40912200-40951400	Weak transcription	Fetal Kidney	kidney
19	chr15:40912600-40941400	Weak transcription	HepG2	liver
20	chr15:40913800-40986000	Weak transcription	A549	lung
21	chr15:40914400-40960000	Weak transcription	NHLF	lung
22	chr15:40914800-40933200	Weak transcription	NHDF-Ad	bronchial
23	chr15:40914800-40942600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr15:40915600-40927200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:40915600-40937000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:40915600-40937000	Weak transcription	HUVEC	blood vessel
27	chr15:40916200-40927800	Weak transcription	HSMM	muscle
28	chr15:40918600-40929200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:40918800-40933400	Strong transcription	Thymus	Thymus
30	chr15:40919200-40935200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
33	chr15:40919800-40938400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr15:40919800-40950200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr15:40920200-40933400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:40921800-40929000	Strong transcription	Fetal Stomach	stomach
37	chr15:40922200-40928600	Strong transcription	Fetal Muscle Leg	muscle
38	chr15:40922200-40930000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:40922400-40938400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:40922600-40926600	Strong transcription	Fetal Intestine Small	intestine
41	chr15:40922600-40927000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:40922600-40928600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr15:40922600-40943800	Weak transcription	Hela-S3	cervix
44	chr15:40922800-40944000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:40922800-40944000	Weak transcription	NHEK	skin
46	chr15:40922800-40954200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr15:40922800-40956000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr15:40923000-40928400	Weak transcription	GM12878-XiMat	blood
49	chr15:40923000-40929600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:40923000-40933000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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