Variant report

Variant	rs12126443
Chromosome Location	chr1:170057917-170057918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:170057709..170058229-chr16:84130062..84130911,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12116788	0.83[EUR][1000 genomes]
rs12117197	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs12117652	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117699	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117892	0.80[CEU][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs12120025	1.00[EUR][1000 genomes]
rs12120443	0.80[CEU][hapmap];0.85[YRI][hapmap]
rs12120968	0.83[EUR][1000 genomes]
rs12121055	1.00[EUR][1000 genomes]
rs12122794	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12128116	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12129144	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12130724	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12131638	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12131740	0.80[CEU][hapmap];0.85[YRI][hapmap]
rs12132530	0.83[EUR][1000 genomes]
rs12132575	0.83[EUR][1000 genomes]
rs12133411	1.00[EUR][1000 genomes]
rs12134995	0.80[CEU][hapmap];0.85[YRI][hapmap]
rs12135070	0.80[CEU][hapmap];0.85[YRI][hapmap]
rs12140845	0.88[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs12141501	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12141522	0.91[EUR][1000 genomes]
rs12142155	1.00[EUR][1000 genomes]
rs12144057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12144085	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12145948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1411465	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863007	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs41272485	0.83[EUR][1000 genomes]
rs488488	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs56147946	0.88[EUR][1000 genomes]
rs688565	0.83[EUR][1000 genomes]
rs7549000	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12126443	MGC9084	cis	multi-tissue	Pritchard
rs12126443	METTL18	cis	Thyroid	GTEx
rs12126443	C1orf156	cis	lymphoblastoid	seeQTL
rs12126443	C1orf156	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170056000-170058200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:170057400-170058000	Enhancers	Ovary	ovary
3	chr1:170057400-170058000	Enhancers	Rectal Mucosa Donor 31	rectum

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