Variant report

Variant	rs12460161
Chromosome Location	chr19:44293986-44293987
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44256154..44259094-chr19:44292665..44294784,3	K562	blood:
2	chr19:44267187..44269964-chr19:44291691..44294557,2	MCF-7	breast:
3	chr19:44287294..44289449-chr19:44292434..44295257,2	MCF-7	breast:
4	chr19:44293403..44294999-chr19:44310086..44311821,2	K562	blood:

Variant related genes	Relation type
ENSG00000105771	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10401170	0.81[ASN][1000 genomes]
rs10401203	0.81[ASN][1000 genomes]
rs10404672	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10405457	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413172	0.88[AFR][1000 genomes]
rs10416361	0.80[EUR][1000 genomes]
rs10421887	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422108	0.87[AFR][1000 genomes]
rs10422990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426528	0.81[ASN][1000 genomes]
rs11665924	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11669175	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670158	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11671215	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12463370	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12974061	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs349046	0.81[ASN][1000 genomes]
rs349047	0.81[ASN][1000 genomes]
rs349048	0.81[ASN][1000 genomes]
rs3760982	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3760983	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3760984	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802199	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802200	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803658	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60184524	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61138927	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104300	0.89[AFR][1000 genomes]
rs8104447	0.81[ASN][1000 genomes]
rs8109478	0.89[AFR][1000 genomes]
rs8109812	0.89[AFR][1000 genomes]
rs8111664	0.81[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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12460161	KCNN4	cis	Whole Blood	GTEx
rs12460161	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44289400-44302600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:44289600-44294800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr19:44289600-44295400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:44289800-44300800	Weak transcription	Placenta	Placenta
5	chr19:44290000-44302400	Weak transcription	NHEK	skin
6	chr19:44290200-44302200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:44293600-44294800	Enhancers	GM12878-XiMat	blood

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