Variant report

Variant	rs2502474
Chromosome Location	chr6:75366301-75366302
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12528062	0.80[EUR][1000 genomes]
rs1537950	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2065884	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2095613	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252269	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2252270	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2252276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485068	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2485070	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2485071	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2485076	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485077	0.80[EUR][1000 genomes]
rs2485078	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485079	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485080	0.80[EUR][1000 genomes]
rs2485081	0.80[EUR][1000 genomes]
rs2485082	0.80[EUR][1000 genomes]
rs2485083	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2485084	0.90[AFR][1000 genomes]
rs2485085	0.90[AFR][1000 genomes]
rs2485086	0.90[AFR][1000 genomes]
rs2485087	0.90[AFR][1000 genomes]
rs2485088	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485091	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2485092	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2485093	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485096	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2502468	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2502470	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2502473	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2502475	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2502476	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2502477	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2502478	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502481	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502482	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502484	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502485	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502486	0.80[EUR][1000 genomes]
rs2502487	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502488	0.80[EUR][1000 genomes]
rs2502490	0.80[EUR][1000 genomes]
rs2502491	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502492	0.80[EUR][1000 genomes]
rs2502493	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502494	0.80[EUR][1000 genomes]
rs2502496	0.97[ASN][1000 genomes]
rs2502503	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2502505	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7739226	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2502474	COL12A1	cis	parietal	SCAN

Chromatin state (count:13 , 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	chr6:75362400-75367000	Weak transcription	NHDF-Ad	bronchial
3	chr6:75362600-75367000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:75363000-75367600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:75363800-75369200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:75364200-75366400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:75364600-75366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:75364600-75366400	Weak transcription	Hela-S3	cervix
9	chr6:75364800-75366800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:75365000-75366800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:75365400-75366600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:75366000-75368600	Enhancers	Osteobl	bone
13	chr6:75366200-75368000	Enhancers	HSMM	muscle

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