Variant report

Variant	rs1421441
Chromosome Location	chr12:106277725-106277726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106275159..106278117-chr12:106531415..106534582,3	MCF-7	breast:
2	chr12:106268251..106270563-chr12:106275858..106278219,2	K562	blood:
3	chr12:106275440..106278338-chr12:106282923..106284779,2	K562	blood:

Variant related genes	Relation type
ENSG00000074590	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10507203	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861526	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861527	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861528	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10861529	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861531	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112776	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112789	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11112791	0.90[EUR][1000 genomes]
rs11615749	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12231942	0.80[JPT][hapmap]
rs12301955	0.88[EUR][1000 genomes]
rs12302909	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12307410	0.85[CEU][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12367295	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12368539	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12423582	0.90[EUR][1000 genomes]
rs12426023	0.87[EUR][1000 genomes]
rs1345544	0.87[EUR][1000 genomes]
rs1345545	0.87[EUR][1000 genomes]
rs1421464	0.85[EUR][1000 genomes]
rs1421467	0.90[EUR][1000 genomes]
rs1541629	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17278606	0.87[EUR][1000 genomes]
rs1862027	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862028	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895104	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2374559	0.87[EUR][1000 genomes]
rs2374561	0.92[CEU][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28635481	0.84[EUR][1000 genomes]
rs4620812	0.83[EUR][1000 genomes]
rs7133626	0.87[EUR][1000 genomes]
rs7297930	0.87[EUR][1000 genomes]
rs7300496	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7300906	0.87[EUR][1000 genomes]
rs7300926	0.87[EUR][1000 genomes]
rs7305359	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73387048	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7960296	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7960880	0.85[EUR][1000 genomes]
rs7964927	0.87[EUR][1000 genomes]
rs7968454	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968564	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980152	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1421441	PAH	cis	parietal	SCAN
rs1421441	GLT8D2	cis	cerebellum	SCAN
rs1421441	CHST11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106276400-106281600	Weak transcription	HSMMtube	muscle
2	chr12:106276600-106282200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:106277000-106278000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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