Variant report

Variant	rs1878264
Chromosome Location	chr11:83579279-83579280
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10898164	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898166	0.87[MEX][hapmap]
rs11233771	0.86[JPT][hapmap]
rs11233774	0.90[JPT][hapmap];0.87[MEX][hapmap]
rs11233776	0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs11822018	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12361034	0.88[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12361320	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12364183	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1540096	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2138567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2374461	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4625494	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7926185	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7937832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs877984	0.82[YRI][hapmap]
rs938536	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898017	chr11:83556067-83583324	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
2	nsv898018	chr11:83556067-83586526	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
3	nsv898019	chr11:83556067-83602367	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
4	nsv898020	chr11:83558738-83602367	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv898021	chr11:83562296-83602367	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv898022	chr11:83562296-83602367	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv898023	chr11:83566115-83602367	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv898024	chr11:83576460-83602367	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1878264	SYTL2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:83576000-83586400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr11:83577200-83584400	Weak transcription	Brain Angular Gyrus	brain
3	chr11:83577200-83584400	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:83577400-83584600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:83577400-83606800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:83577800-83584400	Weak transcription	Brain Anterior Caudate	brain
7	chr11:83578000-83606800	Weak transcription	Brain Substantia Nigra	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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