Variant report

Variant	rs268044
Chromosome Location	chr12:45363545-45363546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1004593	0.84[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10880693	0.95[CEU][hapmap]
rs10880725	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11182707	0.94[CEU][hapmap]
rs1224434	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1224435	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1224438	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1224439	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1224440	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1224442	0.83[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1224444	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1224445	0.83[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1224446	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1224447	0.81[EUR][1000 genomes]
rs1224448	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1224449	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1506677	0.81[EUR][1000 genomes]
rs1826711	0.83[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1921550	0.90[EUR][1000 genomes]
rs1921551	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2055673	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2055674	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2468347	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2544101	0.83[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2544102	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs2643136	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2643137	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2643138	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2643139	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643140	0.84[CHB][hapmap]
rs2643141	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643142	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643143	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643144	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643145	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643147	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2643148	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2643149	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2658972	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs268046	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs268047	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs268048	0.92[EUR][1000 genomes]
rs2710419	0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2710452	0.81[EUR][1000 genomes]
rs2731034	0.86[LWK][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2731037	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2731038	0.83[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2731039	0.83[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2731041	0.88[AMR][1000 genomes]
rs2731042	0.88[AMR][1000 genomes]
rs2731043	0.85[AMR][1000 genomes]
rs2731044	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2731048	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2731049	0.83[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2731050	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2731051	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2731052	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs370814	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs374871	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847982	0.95[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4312124	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs440884	0.95[CEU][hapmap]
rs7295673	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899049	chr12:45299202-45376053	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	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
3	nsv899051	chr12:45307633-45376053	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv527565	chr12:45319767-45365812	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3407092	chr12:45342734-45368068	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv469365	chr12:45353367-45388817	Enhancers Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv558751	chr12:45353367-45388817	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv469366	chr12:45357804-45386398	Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv558752	chr12:45357804-45386398	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv2323636	chr12:45363544-45363547	Enhancers	n/a	n/a	inside rSNPs	diseases
14	esv2504170	chr12:45363545-45363547	Enhancers	n/a	n/a	inside rSNPs	diseases
15	nsv469367	chr12:45363545-45400614	Enhancers Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	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
rs268044	NELL2	cis	Adipose Subcutaneous	GTEx
rs268044	NELL2	cis	Artery Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45361800-45364200	Enhancers	Dnd41	blood
2	chr12:45362000-45364200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:45362000-45364200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:45362200-45364000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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