Variant report

Variant	rs1878512
Chromosome Location	chr2:21420358-21420359
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10169543	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193924	1.00[ASN][1000 genomes]
rs10204476	1.00[ASN][1000 genomes]
rs10205003	1.00[ASN][1000 genomes]
rs10221768	1.00[ASN][1000 genomes]
rs10221876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897480	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618122	0.83[AFR][1000 genomes]
rs12712923	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712940	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397898	1.00[ASN][1000 genomes]
rs13411597	0.88[EUR][1000 genomes]
rs13419611	1.00[ASN][1000 genomes]
rs1367119	0.86[EUR][1000 genomes]
rs1367120	0.86[EUR][1000 genomes]
rs1652416	0.88[EUR][1000 genomes]
rs1652417	0.88[EUR][1000 genomes]
rs1652419	0.87[EUR][1000 genomes]
rs1652420	0.87[EUR][1000 genomes]
rs1652421	0.87[EUR][1000 genomes]
rs1652422	0.87[EUR][1000 genomes]
rs1652423	0.83[EUR][1000 genomes]
rs17041988	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17042000	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712246	0.80[EUR][1000 genomes]
rs1712247	0.87[EUR][1000 genomes]
rs1712248	0.85[EUR][1000 genomes]
rs1712250	0.88[EUR][1000 genomes]
rs1712251	0.88[EUR][1000 genomes]
rs312936	0.90[EUR][1000 genomes]
rs312944	0.83[EUR][1000 genomes]
rs312979	0.87[EUR][1000 genomes]
rs312981	0.87[EUR][1000 genomes]
rs312982	0.87[EUR][1000 genomes]
rs312983	0.86[EUR][1000 genomes]
rs312984	0.87[EUR][1000 genomes]
rs312985	0.87[EUR][1000 genomes]
rs34002646	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34125138	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36047821	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365946	1.00[ASN][1000 genomes]
rs367162	1.00[ASN][1000 genomes]
rs380240	1.00[ASN][1000 genomes]
rs403880	1.00[ASN][1000 genomes]
rs428696	1.00[ASN][1000 genomes]
rs431493	1.00[ASN][1000 genomes]
rs432483	1.00[ASN][1000 genomes]
rs4505563	1.00[ASN][1000 genomes]
rs453862	1.00[ASN][1000 genomes]
rs4542883	1.00[ASN][1000 genomes]
rs4542884	1.00[ASN][1000 genomes]
rs4560142	0.87[EUR][1000 genomes]
rs4591370	0.87[EUR][1000 genomes]
rs4596008	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473269	0.88[EUR][1000 genomes]
rs477146	0.88[EUR][1000 genomes]
rs478442	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs483621	0.88[EUR][1000 genomes]
rs486246	0.89[EUR][1000 genomes]
rs487858	0.89[EUR][1000 genomes]
rs490757	0.86[EUR][1000 genomes]
rs492255	0.87[EUR][1000 genomes]
rs494315	0.89[EUR][1000 genomes]
rs494465	0.89[EUR][1000 genomes]
rs502323	0.89[EUR][1000 genomes]
rs504091	0.88[EUR][1000 genomes]
rs504616	0.85[EUR][1000 genomes]
rs506585	0.88[EUR][1000 genomes]
rs507616	0.88[EUR][1000 genomes]
rs522250	0.88[EUR][1000 genomes]
rs522822	0.89[EUR][1000 genomes]
rs522963	0.87[EUR][1000 genomes]
rs525172	0.87[EUR][1000 genomes]
rs527034	0.87[EUR][1000 genomes]
rs527259	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs529396	0.87[EUR][1000 genomes]
rs529697	0.88[EUR][1000 genomes]
rs530474	0.87[EUR][1000 genomes]
rs531380	0.88[EUR][1000 genomes]
rs532225	0.88[EUR][1000 genomes]
rs532300	0.87[EUR][1000 genomes]
rs533211	0.87[EUR][1000 genomes]
rs533772	0.87[EUR][1000 genomes]
rs539845	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540897	0.86[EUR][1000 genomes]
rs541569	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs544039	1.00[CEU][hapmap]
rs544450	0.87[EUR][1000 genomes]
rs547179	0.86[EUR][1000 genomes]
rs547235	0.87[EUR][1000 genomes]
rs548506	0.87[EUR][1000 genomes]
rs557197	0.87[EUR][1000 genomes]
rs558130	0.86[EUR][1000 genomes]
rs558342	0.88[EUR][1000 genomes]
rs559318	0.87[EUR][1000 genomes]
rs559967	0.88[EUR][1000 genomes]
rs560408	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs560522	0.87[EUR][1000 genomes]
rs561850	0.88[EUR][1000 genomes]
rs563719	0.88[EUR][1000 genomes]
rs563752	0.88[EUR][1000 genomes]
rs569014	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs570033	0.88[EUR][1000 genomes]
rs572246	0.83[EUR][1000 genomes]
rs573314	0.87[EUR][1000 genomes]
rs574461	0.89[EUR][1000 genomes]
rs66774912	1.00[ASN][1000 genomes]
rs67599264	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578527	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578637	1.00[ASN][1000 genomes]
rs9798358	0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873728	chr2:21250914-21460786	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1878512	FKBP1B	cis	cerebellum	SCAN
rs1878512	MSGN1	cis	cerebellum	SCAN
rs1878512	FKBP1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:21416200-21421400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:21416200-21424400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:21416600-21420600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:21417800-21421000	Enhancers	Brain Substantia Nigra	brain
5	chr2:21418600-21422800	Weak transcription	Fetal Intestine Large	intestine
6	chr2:21419400-21421200	Enhancers	Fetal Brain Male	brain
7	chr2:21419600-21421000	Enhancers	Brain Cingulate Gyrus	brain
8	chr2:21419600-21421800	Enhancers	Brain Hippocampus Middle	brain
9	chr2:21419800-21421000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:21420000-21420400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
11	chr2:21420200-21420800	Enhancers	Brain Anterior Caudate	brain

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