Variant report

Variant	rs1224438
Chromosome Location	chr12:45398041-45398042
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1004593	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10880693	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10880725	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11182702	1.00[CHB][hapmap]
rs11182707	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1224434	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1224435	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1224439	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1224440	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1224442	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1224444	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1224445	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1224446	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1224447	0.87[EUR][1000 genomes]
rs1224448	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1224449	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1826711	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1921550	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1921551	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2055673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs2055674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs2468347	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2544101	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2544114	0.87[ASN][1000 genomes]
rs2643136	0.92[CEU][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2643137	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2643138	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2643139	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2643141	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2643142	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2643143	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2643144	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2643145	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2643147	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2643148	0.89[EUR][1000 genomes]
rs2643149	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2658972	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs268044	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs268046	0.82[EUR][1000 genomes]
rs268047	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs268048	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2710419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs2731034	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2731037	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731038	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731039	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731041	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2731042	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2731043	0.80[AMR][1000 genomes]
rs2731044	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2731048	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731049	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731050	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731051	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2731052	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs370814	0.88[EUR][1000 genomes]
rs374871	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3847982	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4312124	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs440884	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7295673	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899050	chr12:45299202-45400614	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv469367	chr12:45363545-45400614	Enhancers Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv558753	chr12:45363545-45400614	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1224438	NELL2	cis	Artery Tibial	GTEx
rs1224438	NELL2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45393000-45412600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:45394600-45406000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:45398000-45398400	Enhancers	HUES6 Cell Line	embryonic stem cell

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