Variant report

Variant	rs2710419
Chromosome Location	chr12:45261606-45261607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1004593	0.85[CEU][hapmap]
rs10880693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182703	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1224434	0.84[EUR][1000 genomes]
rs1224438	0.84[EUR][1000 genomes]
rs1224439	0.84[EUR][1000 genomes]
rs1224442	0.88[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs1224445	0.88[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs1506677	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1826711	0.88[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs1921550	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544101	0.88[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs2643136	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2643138	0.84[EUR][1000 genomes]
rs2658972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268044	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs268046	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs268047	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs268048	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2710452	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2731034	0.85[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs2731038	0.88[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs2731039	0.88[CEU][hapmap]
rs2731049	0.88[CEU][hapmap]
rs370814	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs374871	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3847982	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs440884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7295673	0.95[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2710419	NELL2	cis	Adipose Subcutaneous	GTEx
rs2710419	NELL2	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45257000-45266800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:45257400-45265200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:45258600-45265600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:45258600-45267800	Weak transcription	Brain Germinal Matrix	brain
5	chr12:45259600-45266000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:45260000-45268000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:45260200-45262800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:45260200-45263200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:45260400-45263000	Weak transcription	Fetal Brain Female	brain
10	chr12:45260400-45264000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:45261200-45264800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:45261200-45265400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:45261400-45263200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:45261600-45262600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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