Variant report

Variant	rs2643140
Chromosome Location	chr12:45418311-45418312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1004593	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10880718	0.83[EUR][1000 genomes]
rs10880725	0.98[ASN][1000 genomes]
rs10880730	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs11182810	0.83[EUR][1000 genomes]
rs11182811	0.83[EUR][1000 genomes]
rs1118481	0.82[EUR][1000 genomes]
rs1224435	0.99[ASN][1000 genomes]
rs1224436	0.92[EUR][1000 genomes]
rs1224440	0.98[ASN][1000 genomes]
rs1224442	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1224444	0.99[ASN][1000 genomes]
rs1224445	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1224446	0.99[ASN][1000 genomes]
rs1224447	0.85[ASN][1000 genomes]
rs1224448	0.97[ASN][1000 genomes]
rs1224449	0.97[ASN][1000 genomes]
rs1495033	0.81[EUR][1000 genomes]
rs1495034	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1495035	0.92[EUR][1000 genomes]
rs1495036	0.93[EUR][1000 genomes]
rs1495042	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1826711	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1857924	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1857925	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1857926	0.82[EUR][1000 genomes]
rs2408140	0.91[EUR][1000 genomes]
rs2468347	0.98[ASN][1000 genomes]
rs2544101	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2544102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643137	0.96[ASN][1000 genomes]
rs2643139	1.00[ASN][1000 genomes]
rs2643141	0.99[ASN][1000 genomes]
rs2643142	1.00[ASN][1000 genomes]
rs2643143	1.00[ASN][1000 genomes]
rs2643144	1.00[ASN][1000 genomes]
rs2643145	1.00[ASN][1000 genomes]
rs2643147	1.00[ASN][1000 genomes]
rs2643148	1.00[ASN][1000 genomes]
rs2643149	1.00[ASN][1000 genomes]
rs2731037	1.00[ASN][1000 genomes]
rs2731038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2731039	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2731040	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731041	0.91[ASN][1000 genomes]
rs2731042	0.91[ASN][1000 genomes]
rs2731043	0.89[ASN][1000 genomes]
rs2731044	0.90[ASN][1000 genomes]
rs2731048	1.00[ASN][1000 genomes]
rs2731049	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2731050	1.00[ASN][1000 genomes]
rs2731051	1.00[ASN][1000 genomes]
rs2731052	1.00[ASN][1000 genomes]
rs2731053	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2731054	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140696	0.86[EUR][1000 genomes]
rs4285943	0.91[EUR][1000 genomes]
rs4312124	0.97[ASN][1000 genomes]
rs4561266	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7963606	0.81[EUR][1000 genomes]
rs7964973	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351644	chr12:45345597-45529449	Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1045857	chr12:45351172-45468784	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv541485	chr12:45351172-45468784	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2643140	NELL2	cis	Adipose Subcutaneous	GTEx
rs2643140	RP11-478B9.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2643140	DBX2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45417400-45419000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
2	chr12:45418200-45418600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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