Variant report

Variant	rs1583060
Chromosome Location	chr15:49681218-49681219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11070685	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap]
rs12708418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898461	0.89[CEU][hapmap]
rs12898877	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12903992	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[EUR][1000 genomes]
rs12914592	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12916078	0.89[CEU][hapmap]
rs13379615	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962418	0.89[CEU][hapmap];0.98[EUR][1000 genomes]
rs16962419	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16962434	0.83[CHB][hapmap]
rs16962436	0.93[YRI][hapmap]
rs1961692	0.91[AFR][1000 genomes]
rs2413943	0.93[YRI][hapmap]
rs2413944	0.93[YRI][hapmap]
rs2413945	0.80[YRI][hapmap]
rs34148901	0.98[EUR][1000 genomes]
rs35001785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4332689	0.93[YRI][hapmap]
rs478500	0.89[CEU][hapmap]
rs6493366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap]
rs6493367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs71467676	0.98[EUR][1000 genomes]
rs7162373	0.93[YRI][hapmap]
rs7166491	0.80[EUR][1000 genomes]
rs7177959	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8026364	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8040116	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9806362	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv442375	chr15:49652524-49684082	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1583060	SECISBP2L	cis	brain	BrainEAC
rs1583060	SECISBP2L	cis	cerebellar cortex	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49673800-49683400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:49676400-49683600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:49676600-49683400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr15:49676800-49683000	Weak transcription	H9 Cell Line	embryonic stem cell

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