Variant report

Variant	rs4924502
Chromosome Location	chr15:41027789-41027790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41026566..41029766-chr15:41030549..41035170,5	K562	blood:

Variant related genes	Relation type
ENSG00000137824	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10518697	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11070283	0.80[AMR][1000 genomes]
rs12148915	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12385982	0.80[AMR][1000 genomes]
rs12442560	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591044	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592524	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12903817	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12907442	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12908316	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12915636	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17674454	0.80[AMR][1000 genomes]
rs17747423	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17747633	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1801321	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2619682	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28866515	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28891195	0.81[AMR][1000 genomes]
rs34305357	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34739056	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35127391	0.83[AMR][1000 genomes]
rs35684277	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4923880	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4924486	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4924492	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924496	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924498	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5030789	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56409425	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59244061	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6492964	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71471880	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7165509	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7175747	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7175905	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7176245	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176590	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7177265	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7180135	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7182499	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029530	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8036891	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8037180	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8038122	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8042386	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs957603	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920676	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4924502	C15orf57	cis	Artery Tibial	GTEx
rs4924502	RP11-111A22.1	cis	lung	GTEx
rs4924502	C15orf57	cis	lung	GTEx
rs4924502	CCDC32	cis	multi-tissue	Pritchard
rs4924502	C15orf57	cis	Adipose Subcutaneous	GTEx
rs4924502	C15orf57	cis	Esophagus Muscularis	GTEx
rs4924502	C15orf57	cis	Artery Aorta	GTEx
rs4924502	C15orf57	cis	Muscle Skeletal	GTEx
rs4924502	C15orf57	cis	Nerve Tibial	GTEx
rs4924502	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs4924502	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs4924502	RAD51	cis	multi-tissue	Pritchard
rs4924502	RP11-111A22.1	cis	Artery Tibial	GTEx
rs4924502	C15orf57	cis	Heart Left Ventricle	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
2	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
3	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
5	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:41012800-41028200	Weak transcription	NHLF	lung
7	chr15:41014600-41029600	Weak transcription	Esophagus	oesophagus
8	chr15:41019200-41035600	Weak transcription	Fetal Heart	heart
9	chr15:41019400-41028600	Weak transcription	Fetal Brain Male	brain
10	chr15:41019400-41036000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:41019400-41046200	Strong transcription	Fetal Stomach	stomach
12	chr15:41019600-41036200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:41019600-41036200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:41020000-41027800	Weak transcription	Psoas Muscle	Psoas
15	chr15:41020000-41029800	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr15:41020000-41036000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:41020000-41043600	Strong transcription	Dnd41	blood
18	chr15:41020200-41027800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:41020200-41030600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:41020400-41027800	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:41020400-41028000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:41020400-41028200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:41020400-41028200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:41020400-41035600	Strong transcription	K562	blood
25	chr15:41020400-41035800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:41020400-41036000	Strong transcription	Fetal Thymus	thymus
27	chr15:41020400-41037600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:41020600-41029600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:41020600-41030800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:41020600-41030800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:41020600-41033600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:41020600-41036000	Strong transcription	Placenta	Placenta
33	chr15:41020600-41036800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:41020600-41037800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr15:41020600-41038200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:41020800-41032600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:41020800-41035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr15:41020800-41035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:41020800-41045400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr15:41021000-41028600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr15:41021400-41030200	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr15:41021400-41033400	Strong transcription	Fetal Brain Female	brain
43	chr15:41021600-41032800	Strong transcription	Osteobl	bone
44	chr15:41021600-41033600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:41021600-41034800	Strong transcription	Fetal Intestine Large	intestine
46	chr15:41021600-41035800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:41021600-41035800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:41021600-41036000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:41021800-41034200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:41021800-41044600	Strong transcription	Brain Germinal Matrix	brain

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