Variant report

Variant	rs12654590
Chromosome Location	chr5:114690323-114690324
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	chr5:114663750..114666147-chr5:114688735..114691561,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10447263	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10463669	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10519405	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519406	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241320	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241323	0.92[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12516512	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12519220	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12657417	0.96[CEU][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1445697	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1455849	0.83[JPT][hapmap];0.84[MEX][hapmap]
rs1455850	0.83[JPT][hapmap];0.84[MEX][hapmap]
rs166566	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17137700	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2416401	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2416402	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2416403	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2416404	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2416406	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2591258	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2605178	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2605179	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs269503	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs269504	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs269505	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs269506	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs269510	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2900093	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34919660	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35900499	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4705524	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4705733	0.91[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7703838	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7704303	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7715232	0.91[CEU][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7721559	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7733943	0.87[AMR][1000 genomes];0.89[EUR][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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12654590	MCC	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114685400-114691400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:114685600-114695800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:114688000-114690400	Weak transcription	Hela-S3	cervix
4	chr5:114689600-114690400	Enhancers	Liver	Liver
5	chr5:114689600-114690400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr5:114690200-114691200	Enhancers	A549	lung
7	chr5:114690200-114691800	Enhancers	Stomach Mucosa	stomach

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