Variant report

Variant	rs10422359
Chromosome Location	chr19:52047077-52047078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52045424..52047924-chr19:52076002..52077795,2	K562	blood:
2	chr19:51795590..51798270-chr19:52046982..52049972,2	K562	blood:

Variant related genes	Relation type
ENSG00000105497	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10409713	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs10419617	0.87[ASN][1000 genomes]
rs1457098	0.83[YRI][hapmap]
rs1551559	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs2124907	0.86[ASN][1000 genomes]
rs2124909	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2124910	0.80[ASW][hapmap];0.83[CHD][hapmap];0.83[YRI][hapmap]
rs2168637	0.91[ASN][1000 genomes]
rs2290660	0.86[ASN][1000 genomes]
rs2305772	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3794986	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4146202	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs4146203	0.82[JPT][hapmap]
rs4802800	0.83[YRI][hapmap]
rs4802807	0.80[ASW][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs7250820	0.91[ASN][1000 genomes]
rs7259990	0.91[ASN][1000 genomes]
rs8100330	0.80[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.91[ASN][1000 genomes]
rs8100538	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs8101887	0.86[ASN][1000 genomes]
rs897783	0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10422359	SIGLEC12	cis	Whole Blood	GTEx
rs10422359	BRSK1	cis	parietal	SCAN
rs10422359	ZNF417	cis	cerebellum	SCAN
rs10422359	SIGLEC12	cis	Artery Tibial	GTEx
rs10422359	SIGLEC12	cis	multi-tissue	Pritchard
rs10422359	ZNF320	cis	cerebellum	SCAN
rs10422359	PPP1R12C	cis	cerebellum	SCAN
rs10422359	SIGLEC5	cis	lymphoblastoid	seeQTL
rs10422359	SIGLEC12	cis	lung	GTEx
rs10422359	ZNF468	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52045200-52049200	Enhancers	K562	blood
2	chr19:52046000-52048800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:52046400-52047200	Weak transcription	Primary B cells from peripheral blood	blood

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