Variant report

Variant	rs6744548
Chromosome Location	chr2:55166094-55166095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55164082..55167109-chr2:55181433..55184478,3	K562	blood:
2	chr2:55164941..55167851-chr2:55169428..55172697,4	K562	blood:
3	chr2:55152934..55155386-chr2:55163705..55166391,2	K562	blood:
4	chr2:55164082..55168413-chr2:55180367..55184478,5	K562	blood:

Variant related genes	Relation type
ENSG00000214595	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10153551	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10153785	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10164886	0.90[ASN][1000 genomes]
rs10176018	0.90[ASN][1000 genomes]
rs10200365	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3821112	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4502460	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6545461	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749322	0.93[LWK][hapmap]
rs6759673	0.89[LWK][hapmap]
rs7574696	1.00[JPT][hapmap]
rs7586885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589959	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590130	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590241	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590265	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606659	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9309261	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808435	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6744548	VRK2	cis	cerebellum	SCAN
rs6744548	CCDC85A	cis	parietal	SCAN
rs6744548	PSME4	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55150000-55168400	Weak transcription	Pancreas	Pancrea
2	chr2:55154200-55166600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:55154400-55168000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:55154800-55167800	Weak transcription	Brain Angular Gyrus	brain
5	chr2:55165800-55169200	Enhancers	Fetal Muscle Leg	muscle

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