Variant report

Variant	rs2658972
Chromosome Location	chr12:45267618-45267619
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:44408858..44409800-chr12:45267480..45268238,2	MCF-7	breast:
2	chr12:45168304..45169119-chr12:45267170..45268311,3	MCF-7	breast:

Extended variants
information (count: 36 )
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];0.81[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]
rs1224445	0.88[CEU][hapmap]
rs1506677	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1826711	0.88[CEU][hapmap]
rs1921550	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544101	0.88[CEU][hapmap]
rs2643136	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2643138	0.84[EUR][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]
rs2710419	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]
rs2710452	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2731034	0.84[CEU][hapmap]
rs2731038	0.88[CEU][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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];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:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs2658972	NELL2	cis	Artery Tibial	GTEx
rs2658972	NELL2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45258600-45267800	Weak transcription	Brain Germinal Matrix	brain
2	chr12:45260000-45268000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:45262000-45267800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:45263000-45269000	Active TSS	Fetal Brain Female	brain
5	chr12:45264800-45271200	Active TSS	Fetal Brain Male	brain
6	chr12:45265600-45268000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:45266000-45270600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr12:45266400-45268600	Active TSS	Brain Angular Gyrus	brain
9	chr12:45266400-45269200	Active TSS	Brain Anterior Caudate	brain
10	chr12:45266800-45267800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:45266800-45268800	Active TSS	Brain Hippocampus Middle	brain
12	chr12:45266800-45269200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr12:45266800-45270800	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr12:45267000-45267800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:45267000-45267800	Active TSS	Primary T cells from cord blood	blood
16	chr12:45267000-45268000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:45267000-45268800	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr12:45267000-45269200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr12:45267200-45268000	Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr12:45267200-45268400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:45267200-45271000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:45267200-45271400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:45267400-45267800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr12:45267400-45268000	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr12:45267400-45268000	Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr12:45267400-45268000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:45267400-45268200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:45267600-45268000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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