Variant report

Variant	rs6427496
Chromosome Location	chr1:159790826-159790827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:159785033..159789161-chr1:159789776..159794459,5	K562	blood:
2	chr1:159789686..159791388-chr1:159893723..159895408,2	K562	blood:
3	chr1:159775540..159777922-chr1:159789657..159792630,2	K562	blood:
4	chr1:159789616..159791750-chr1:159794351..159797260,2	K562	blood:

Variant related genes	Relation type
ENSG00000158714	Chromatin interaction
ENSG00000158710	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11265282	0.81[TSI][hapmap]
rs11591079	1.00[CEU][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12088352	0.84[EUR][1000 genomes]
rs2494495	0.88[CEU][hapmap]
rs2501343	0.83[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap]
rs4656246	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55739401	0.87[EUR][1000 genomes]
rs55742616	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60205880	0.87[EUR][1000 genomes]
rs61821619	0.83[AMR][1000 genomes]
rs61821621	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61821622	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61821626	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61821627	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61821659	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61823160	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61823162	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61823163	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61823164	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61823165	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72700609	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72700610	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72700611	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72700615	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72700621	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72700626	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72700627	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72700628	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72700632	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72700634	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7519854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7525794	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7527418	0.88[EUR][1000 genomes]
rs7528163	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7549918	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv521503	chr1:159762120-159795478	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6427496	HAPLN2	cis	cerebellum	SCAN
rs6427496	OR6N2	cis	cerebellum	SCAN
rs6427496	OLFML2B	cis	cerebellum	SCAN
rs6427496	COPA	cis	cerebellum	SCAN
rs6427496	FCRL6	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159774800-159796000	Weak transcription	Right Atrium	heart
2	chr1:159775800-159793400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:159779600-159794800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:159785400-159792800	Weak transcription	Spleen	Spleen
5	chr1:159785800-159791000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:159787400-159791000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:159788600-159793000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:159789800-159793000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:159790800-159791200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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