Variant report

Variant	rs2412524
Chromosome Location	chr15:40793261-40793262
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40789702..40793899-chr15:40802454..40805435,6	K562	blood:
2	chr15:40790726..40793810-chr15:40802454..40804415,3	K562	blood:
3	chr15:40789021..40791161-chr15:40792541..40794393,2	K562	blood:
4	chr15:40788119..40791373-chr15:40792541..40795559,4	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1051482	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs10851396	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs11070279	0.87[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs11852527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853333	0.87[TSI][hapmap]
rs11857247	0.96[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs12148185	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs12907448	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs12908114	0.87[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs12915563	0.83[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs12916323	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1453183	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs1901774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123534	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2412545	0.83[CEU][hapmap];0.86[MEX][hapmap]
rs3213999	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34750756	0.83[AMR][1000 genomes]
rs35030447	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36122190	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4457966	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs5030783	0.83[CEU][hapmap]
rs61048252	0.84[EUR][1000 genomes]
rs62018030	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62018046	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62018048	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62018051	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7164385	0.85[EUR][1000 genomes]
rs7181909	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72733469	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs731640	0.91[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs733299	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8025458	0.92[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs8028910	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9672313	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs9806410	0.91[CEU][hapmap];0.89[TSI][hapmap]
rs999197	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs2412524	PAK6	cis	parietal	SCAN
rs2412524	C15orf57	cis	Adipose Subcutaneous	GTEx
rs2412524	PLA2G4E	cis	parietal	SCAN
rs2412524	C15orf57	cis	cerebellum	SCAN
rs2412524	MGC20481	cis	multi-tissue	Pritchard
rs2412524	C15orf57	cis	lung	GTEx
rs2412524	C15orf57	cis	lymphoblastoid	seeQTL
rs2412524	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs2412524	LPCAT4	cis	parietal	SCAN
rs2412524	C15orf57	cis	parietal	SCAN
rs2412524	RP11-111A22.1	cis	lung	GTEx
rs2412524	ZFYVE19	cis	cerebellum	SCAN
rs2412524	C15orf57	cis	Cerebellum	GTEx
rs2412524	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2412524	C15orf23	cis	cerebellum	SCAN
rs2412524	DISP2	cis	Thyroid	GTEx
rs2412524	MRPL42P5	cis	multi-tissue	Pritchard
rs2412524	C15orf57	cis	Esophagus Muscularis	GTEx
rs2412524	ZFYVE19	cis	parietal	SCAN
rs2412524	C15orf23	cis	parietal	SCAN
rs2412524	C15orf57	cis	Artery Tibial	GTEx
rs2412524	IVD	cis	cerebellum	SCAN
rs2412524	CCDC32	cis	lesional skin	skin_eQTL
rs2412524	CCDC32	cis	multi-tissue	Pritchard
rs2412524	CCDC32	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40786600-40799200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:40791400-40794000	Enhancers	Hela-S3	cervix
3	chr15:40791600-40793800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:40792000-40793600	Enhancers	NHLF	lung
5	chr15:40792000-40794000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr15:40792200-40793800	Enhancers	HMEC	breast
7	chr15:40792200-40794000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:40792200-40794000	Enhancers	NHEK	skin
9	chr15:40792200-40794000	Enhancers	Osteobl	bone
10	chr15:40792400-40794000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:40792400-40794000	Enhancers	NH-A	brain
12	chr15:40792600-40793600	Enhancers	HUVEC	blood vessel
13	chr15:40792600-40794000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:40793000-40793600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:40793000-40793600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:40793000-40793600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:40793200-40793400	Enhancers	K562	blood
18	chr15:40793200-40793600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:40793200-40794000	Enhancers	HSMM	muscle
20	chr15:40793200-40794000	Enhancers	NHDF-Ad	bronchial

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