Variant report

Variant	rs12198041
Chromosome Location	chr6:55986145-55986146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1011277	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925165	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1925166	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1925170	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1925174	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925175	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1998699	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2076473	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2397203	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3846919	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4374814	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4452633	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4612164	0.80[EUR][1000 genomes]
rs4715576	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715577	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4715578	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715580	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6920461	0.84[EUR][1000 genomes]
rs6926301	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6927562	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9296827	0.81[EUR][1000 genomes]
rs9296831	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357887	0.81[EUR][1000 genomes]
rs9367676	0.80[EUR][1000 genomes]
rs9370479	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370482	0.81[EUR][1000 genomes]
rs9396173	0.81[EUR][1000 genomes]
rs9475556	0.80[EUR][1000 genomes]
rs9475564	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9475565	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1029182	chr6:55910866-55991956	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12198041	COL21A1	cis	Nerve Tibial	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55920600-56018400	Weak transcription	Ovary	ovary
2	chr6:55967800-56008600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:55977800-55990000	Weak transcription	Placenta	Placenta
4	chr6:55979200-55989000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:55979200-55998400	Weak transcription	Aorta	Aorta
6	chr6:55979200-55998400	Weak transcription	Fetal Stomach	stomach
7	chr6:55980800-55992600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:55983200-55988800	Strong transcription	Fetal Lung	lung
9	chr6:55984000-56037000	Weak transcription	Fetal Kidney	kidney
10	chr6:55984600-55986600	Strong transcription	Fetal Muscle Leg	muscle

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