Variant report

Variant	rs1862028
Chromosome Location	chr12:106281355-106281356
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	chr12:106279574..106282176-chr12:106284650..106286937,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10507203	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861526	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861527	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861528	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10861529	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861530	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861531	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11112776	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112789	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11112791	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11615749	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12231942	0.80[JPT][hapmap]
rs12301955	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12302909	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12307410	0.85[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs12367295	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12368539	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12423582	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12426023	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1345544	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1345545	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1421441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421464	0.86[EUR][1000 genomes]
rs1421467	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1541629	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17278606	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1862027	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895104	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2374559	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2374561	0.92[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs28635481	0.84[EUR][1000 genomes]
rs4620812	0.84[EUR][1000 genomes]
rs7133626	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7297930	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7300496	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7300906	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7300926	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7305359	0.87[EUR][1000 genomes]
rs73387048	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7960296	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7960880	0.86[EUR][1000 genomes]
rs7964927	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7968454	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968564	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980152	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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
rs1862028	PAH	cis	parietal	SCAN
rs1862028	GLT8D2	cis	cerebellum	SCAN
rs1862028	CHST11	cis	parietal	SCAN

Chromatin state (count:7 , 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	chr12:106280200-106284200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:106280600-106284000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:106280800-106281600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:106281000-106281400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr12:106281000-106283200	Weak transcription	Aorta	Aorta

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