Variant report

Variant	rs2643154
Chromosome Location	chr12:45466344-45466345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1004593	0.84[CEU][hapmap]
rs11182820	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182833	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182841	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1224442	0.88[CEU][hapmap]
rs1224445	0.88[CEU][hapmap]
rs12366891	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1826711	0.88[CEU][hapmap]
rs2544101	0.88[CEU][hapmap]
rs2544108	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2544109	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2544110	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2544113	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544114	0.93[EUR][1000 genomes]
rs2643136	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs2643155	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2658972	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs2731033	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2731034	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs2731038	0.88[CEU][hapmap]
rs2731039	0.88[CEU][hapmap]
rs2731045	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731046	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731049	0.88[CEU][hapmap]
rs41427348	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs440884	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs7295673	0.95[CEU][hapmap]

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
rs2643154	NELL2	cis	Artery Tibial	GTEx
rs2643154	NELL2	cis	Adipose Subcutaneous	GTEx
rs2643154	PPHLN1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45465400-45466600	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr12:45465600-45466600	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr12:45465600-45466800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:45465800-45466600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr12:45465800-45466800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr12:45465800-45466800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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