Variant report

Variant	rs12289688
Chromosome Location	chr11:83687873-83687874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10160486	0.87[CEU][hapmap]
rs11233848	1.00[MEX][hapmap]
rs11233853	1.00[MEX][hapmap]
rs11233863	1.00[MEX][hapmap]
rs11233873	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs11233878	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11233885	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11233886	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11233887	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11233888	0.98[EUR][1000 genomes]
rs11233889	0.95[EUR][1000 genomes]
rs11233891	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11233892	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11501812	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12270426	1.00[MEX][hapmap]
rs12272484	1.00[MEX][hapmap]
rs12273926	1.00[MEX][hapmap]
rs12274345	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12275051	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12275529	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12280070	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12282675	1.00[EUR][1000 genomes]
rs12283683	1.00[CEU][hapmap]
rs12286025	1.00[CEU][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12286565	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12290311	0.97[EUR][1000 genomes]
rs12291418	1.00[MEX][hapmap]
rs12292970	1.00[MEX][hapmap]
rs12294444	0.87[CEU][hapmap]
rs12294547	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12295053	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12575693	0.95[EUR][1000 genomes]
rs1351729	0.89[TSI][hapmap]
rs1384754	1.00[MEX][hapmap]
rs1483402	1.00[MEX][hapmap]
rs1483403	1.00[MEX][hapmap]
rs1483410	0.88[EUR][1000 genomes]
rs17146592	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2062208	0.82[GIH][hapmap]
rs2514164	0.82[AFR][1000 genomes]
rs28673785	0.90[EUR][1000 genomes]
rs4433587	0.89[EUR][1000 genomes]
rs56209818	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7115622	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7131673	1.00[MEX][hapmap]
rs73513704	0.98[EUR][1000 genomes]
rs7932501	1.00[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898025	chr11:83658909-83796678	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
2	nsv1039924	chr11:83662904-83993497	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv541102	chr11:83662904-83993497	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv898026	chr11:83685801-83789540	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv983047	chr11:83687828-83689052	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:83683800-83692000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:83684000-83690400	Weak transcription	Brain Hippocampus Middle	brain
3	chr11:83684000-83690600	Weak transcription	Brain Substantia Nigra	brain
4	chr11:83686400-83688600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:83686800-83688400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr11:83686800-83688600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:83687000-83688400	Enhancers	Brain Anterior Caudate	brain
8	chr11:83687400-83690600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:83687600-83690600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:83687600-83690600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:83687600-83693000	Weak transcription	Brain Angular Gyrus	brain

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