Variant report

Variant	rs12871787
Chromosome Location	chr13:30232353-30232354
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30165310..30167432-chr13:30231633..30234187,2	K562	blood:
2	chr13:30167314..30169877-chr13:30230772..30232474,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11838567	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11840911	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11841138	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11841148	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11841157	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11841439	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11843086	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11843900	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12860598	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12864518	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12866053	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12866393	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12873225	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12876062	0.82[EUR][1000 genomes]
rs1576607	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34203921	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34622544	0.82[EUR][1000 genomes]
rs34715453	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34825298	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35243951	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35253788	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35331003	0.82[EUR][1000 genomes]
rs35409650	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35502883	0.93[EUR][1000 genomes]
rs36018849	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36182222	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs71434734	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7987685	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7992475	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7993901	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9579456	0.82[EUR][1000 genomes]
rs9579458	0.82[EUR][1000 genomes]
rs9579460	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv980	chr13:30200197-30236915	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv510577	chr13:30213612-30254316	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12871787	LOC374491	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30222800-30232800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr13:30222800-30232800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr13:30228400-30233800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:30231000-30232800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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