Variant report

Variant	rs16933090
Chromosome Location	chr11:16455794-16455795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1393928	0.81[CEU][hapmap]
rs1503442	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[ASN][1000 genomes]
rs16932975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs17470624	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17554301	0.93[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs17554911	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4756846	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4757400	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs55820833	0.94[EUR][1000 genomes]
rs56030154	0.94[EUR][1000 genomes]
rs57463944	0.94[EUR][1000 genomes]
rs58769283	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61404451	1.00[ASN][1000 genomes]
rs61469208	0.81[ASN][1000 genomes]
rs72871370	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72871390	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72871402	0.96[EUR][1000 genomes]
rs72873303	0.97[EUR][1000 genomes]
rs72873307	0.97[EUR][1000 genomes]
rs73429701	1.00[ASN][1000 genomes]
rs73431671	1.00[ASN][1000 genomes]
rs73431673	1.00[ASN][1000 genomes]
rs73431677	1.00[ASN][1000 genomes]
rs73431679	1.00[ASN][1000 genomes]
rs73431686	1.00[ASN][1000 genomes]
rs73431697	1.00[ASN][1000 genomes]
rs73433503	1.00[ASN][1000 genomes]
rs73433517	1.00[ASN][1000 genomes]
rs73433521	1.00[ASN][1000 genomes]
rs73433526	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73433528	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73433538	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73433558	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73433560	1.00[ASN][1000 genomes]
rs7925853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs7938702	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs924748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529731	chr11:16122782-16468170	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv553566	chr11:16329009-16799044	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv832075	chr11:16391700-16490934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv897016	chr11:16455794-16691743	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16933090	SPTY2D1	cis	cerebellum	SCAN
rs16933090	PDE3B	cis	cerebellum	SCAN
rs16933090	PARVA	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16452800-16461400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:16453800-16461200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:16455200-16456000	Enhancers	Adipose Nuclei	Adipose
4	chr11:16455200-16456000	Enhancers	Fetal Intestine Large	intestine

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