Variant report

Variant	rs1537950
Chromosome Location	chr6:75380893-75380894
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12527794	0.84[ASN][1000 genomes]
rs12528062	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12529893	0.84[ASN][1000 genomes]
rs2065884	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2095613	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2152712	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2152713	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2243712	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2252269	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252270	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2252276	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2485067	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2485070	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2485071	0.81[TSI][hapmap];0.88[YRI][hapmap]
rs2485076	0.85[AFR][1000 genomes]
rs2485077	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485078	0.86[AFR][1000 genomes]
rs2485080	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485081	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485082	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485083	0.83[AFR][1000 genomes]
rs2485084	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485085	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485086	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2485087	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485088	0.86[AFR][1000 genomes]
rs2485089	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485091	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485092	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485093	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2485094	0.85[ASN][1000 genomes]
rs2485096	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2502468	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2502470	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502473	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502474	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2502475	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2502477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2502478	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2502481	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2502482	0.89[AFR][1000 genomes]
rs2502484	0.89[AFR][1000 genomes]
rs2502485	0.86[AFR][1000 genomes]
rs2502486	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2502487	0.86[AFR][1000 genomes]
rs2502488	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2502489	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2502490	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2502491	0.86[AFR][1000 genomes]
rs2502492	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2502493	0.85[AFR][1000 genomes]
rs2502494	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2502503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502533	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2502537	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4235888	0.82[CEU][hapmap]
rs4235889	0.82[CEU][hapmap]
rs62438603	0.82[AMR][1000 genomes]
rs6453767	0.82[CEU][hapmap]
rs7739226	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9343210	0.84[ASN][1000 genomes]
rs9360837	0.87[AMR][1000 genomes];0.82[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
rs1537950	COL12A1	cis	parietal	SCAN
rs1537950	SPTLC2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75380200-75381800	Enhancers	Osteobl	bone
2	chr6:75380400-75381000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:75380400-75381200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:75380400-75381400	Enhancers	NHDF-Ad	bronchial
5	chr6:75380800-75381200	Enhancers	NHLF	lung
6	chr6:75380800-75381400	Enhancers	HSMM	muscle
7	chr6:75380800-75382200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:75380800-75382200	Enhancers	Aorta	Aorta
9	chr6:75380800-75382200	Enhancers	Fetal Lung	lung
10	chr6:75380800-75382200	Enhancers	Ovary	ovary
11	chr6:75380800-75382400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:75380800-75382800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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