Variant report

Variant	rs2502473
Chromosome Location	chr6:75367272-75367273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12528062	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1537950	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2065884	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2095613	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2152712	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2152713	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2243712	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2252269	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252270	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2252276	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2485067	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2485070	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2485071	0.84[TSI][hapmap];0.84[YRI][hapmap]
rs2485076	0.86[AFR][1000 genomes]
rs2485077	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485078	0.87[AFR][1000 genomes]
rs2485080	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485081	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485082	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485083	0.84[AFR][1000 genomes]
rs2485084	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485085	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485086	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2485087	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485088	0.87[AFR][1000 genomes]
rs2485089	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485091	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485092	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2485093	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2485096	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2502468	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2502470	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502474	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2502475	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2502476	0.81[AFR][1000 genomes]
rs2502477	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2502478	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2502481	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2502482	0.90[AFR][1000 genomes]
rs2502484	0.90[AFR][1000 genomes]
rs2502485	0.87[AFR][1000 genomes]
rs2502486	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2502487	0.87[AFR][1000 genomes]
rs2502488	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2502489	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2502490	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2502491	0.87[AFR][1000 genomes]
rs2502492	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2502493	0.86[AFR][1000 genomes]
rs2502494	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2502503	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502505	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502533	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2502537	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4235888	0.82[CEU][hapmap]
rs4235889	0.82[CEU][hapmap]
rs61419803	0.82[ASN][1000 genomes]
rs6453767	0.82[CEU][hapmap]
rs7739226	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9360837	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520746	chr6:75211546-75691814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv917283	chr6:75234428-75641440	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv830694	chr6:75245483-75446282	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1027029	chr6:75364848-75417967	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1015675	chr6:75365189-75422887	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2502473	COL12A1	cis	parietal	SCAN
rs2502473	SPTLC2	trans	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75360200-75367800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:75363000-75367600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:75363800-75369200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:75366000-75368600	Enhancers	Osteobl	bone
5	chr6:75366200-75368000	Enhancers	HSMM	muscle
6	chr6:75366400-75367800	Enhancers	Hela-S3	cervix
7	chr6:75366400-75368400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr6:75366600-75367600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:75366800-75367400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:75367000-75367600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:75367000-75368000	Enhancers	HSMMtube	muscle
12	chr6:75367000-75368000	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links