Variant report

Variant	rs11233776
Chromosome Location	chr11:83592513-83592514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10751100	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs10792696	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898164	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs10898166	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10898168	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10898175	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10898178	0.85[GIH][hapmap]
rs11233771	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11537255	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11822018	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12361034	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs12361320	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12364183	0.81[EUR][1000 genomes]
rs1400315	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1483393	0.85[GIH][hapmap]
rs1540096	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1878264	0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs1878265	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs2102784	0.89[AFR][1000 genomes]
rs2138567	0.86[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2374461	0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs28600785	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625494	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7112497	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7112521	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7926185	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7927301	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7933375	1.00[GIH][hapmap]
rs7937832	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs7939073	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs938536	0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[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	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
2	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
3	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
4	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
5	nsv898023	chr11:83566115-83602367	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv898024	chr11:83576460-83602367	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv468765	chr11:83591584-83620940	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv555607	chr11:83591584-83620940	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11233776	SYTL2	cis	parietal	SCAN
rs11233776	NIT2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:83577400-83606800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:83578000-83606800	Weak transcription	Brain Substantia Nigra	brain
3	chr11:83585200-83606600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:83585200-83606600	Weak transcription	Brain Hippocampus Middle	brain

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