Variant report

Variant	rs12459644
Chromosome Location	chr19:52039846-52039847
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:51974430..51976310-chr19:52037889..52040847,2	K562	blood:
2	chr19:52036245..52040151-chr19:52052262..52055120,4	K562	blood:
3	chr19:52038651..52041240-chr19:52044737..52046405,3	K562	blood:
4	chr19:52034313..52037413-chr19:52038588..52042803,4	K562	blood:

Variant related genes	Relation type
ENSG00000105492	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10221507	0.87[ASN][1000 genomes]
rs11084084	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs11084085	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12459648	0.98[ASN][1000 genomes]
rs12459809	0.89[CHB][hapmap];0.89[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460000	1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs12460678	0.84[ASN][1000 genomes]
rs12461433	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12461762	0.90[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12461773	0.87[ASN][1000 genomes]
rs12461985	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12462094	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12462104	0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12463035	0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12609761	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs12609762	0.95[ASN][1000 genomes]
rs12609771	0.93[ASN][1000 genomes]
rs17239287	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1993462	0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2005199	0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2290659	0.87[ASN][1000 genomes]
rs2290661	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2305771	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4801872	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4801875	1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs4802802	0.84[ASN][1000 genomes]
rs4802803	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4802808	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802809	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55985514	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56118193	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113284	0.87[ASN][1000 genomes]
rs62113286	0.98[ASN][1000 genomes]
rs62113288	0.98[ASN][1000 genomes]
rs62113289	0.98[ASN][1000 genomes]
rs62116202	0.84[ASN][1000 genomes]
rs62116203	0.84[ASN][1000 genomes]
rs62116204	0.84[ASN][1000 genomes]
rs62116205	0.87[ASN][1000 genomes]
rs73559130	0.84[ASN][1000 genomes]
rs73559152	0.87[ASN][1000 genomes]
rs73559183	0.89[ASN][1000 genomes]
rs8105348	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113077	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807825	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12459644	SIGLEC5	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52035400-52044800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:52038200-52040600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:52039400-52040000	Enhancers	GM12878-XiMat	blood

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