Variant report

Variant	rs1521102
Chromosome Location	chr2:141988398-141988399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10188773	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1118042	0.87[CEU][hapmap]
rs13424853	0.87[CEU][hapmap]
rs16845762	0.87[CEU][hapmap]
rs2049153	0.91[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2139149	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs300369	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs300406	0.88[EUR][1000 genomes]
rs384507	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs387846	0.90[CHB][hapmap]
rs389593	0.89[CHB][hapmap]
rs399117	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs416307	0.88[EUR][1000 genomes]
rs423807	0.88[EUR][1000 genomes]
rs434276	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs442660	0.87[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs4954697	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6712429	0.87[CEU][hapmap];0.84[CHD][hapmap];0.86[TSI][hapmap]
rs6719988	0.87[CEU][hapmap]
rs7560336	0.90[CEU][hapmap]
rs7560604	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9283437	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs955681	0.80[CHB][hapmap]
rs962904	0.86[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs969575	0.89[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583198	chr2:141510791-142150620	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003799	chr2:141803314-142033675	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1009434	chr2:141832339-142156180	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1005236	chr2:141860005-142047695	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv535948	chr2:141860005-142047695	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3332011	chr2:141974269-141990959	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1521102	LRRC66	trans	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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