Variant report

Variant	rs2897590
Chromosome Location	chr12:43151728-43151729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:43144917..43147362-chr12:43148881..43152996,3	MCF-7	breast:
2	chr12:42983007..42984827-chr12:43150919..43152450,2	MCF-7	breast:
3	chr12:43149824..43152359-chr12:43167562..43169768,2	MCF-7	breast:
4	chr12:43128007..43129879-chr12:43150187..43151770,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139174	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10506219	0.92[EUR][1000 genomes]
rs11181672	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181673	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181674	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181675	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181676	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181677	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181678	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11181679	0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11181680	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11181681	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11181682	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12302566	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12311080	0.91[EUR][1000 genomes]
rs12313884	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12319782	0.93[EUR][1000 genomes]
rs1356421	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1356422	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1356423	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1607251	0.83[EUR][1000 genomes]
rs1914486	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1914487	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2203734	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57284063	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60367750	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61924560	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61926694	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7137412	0.91[EUR][1000 genomes]
rs7953873	0.84[EUR][1000 genomes]
rs7954424	0.83[EUR][1000 genomes]
rs7962745	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7963132	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7963276	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7963631	0.85[EUR][1000 genomes]
rs868765	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs870972	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs955918	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832389	chr12:43003361-43173896	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv558748	chr12:43151728-43152847	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2897590	NELL2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43140800-43152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:43149600-43152200	Enhancers	HSMM	muscle
3	chr12:43149600-43153800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr12:43149600-43154800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr12:43149600-43156400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:43149800-43153200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr12:43149800-43153600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:43149800-43154000	Enhancers	H9 Cell Line	embryonic stem cell
9	chr12:43149800-43155200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:43149800-43156600	Enhancers	HMEC	breast
11	chr12:43150000-43151800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:43150000-43151800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:43150000-43153800	Enhancers	NHEK	skin
14	chr12:43150200-43152000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:43150200-43152000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:43150200-43152000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:43150200-43152200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:43150200-43152200	Enhancers	Osteobl	bone
19	chr12:43150200-43154000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr12:43150200-43154400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:43150200-43154400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr12:43150200-43155200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:43150400-43151800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:43150400-43151800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:43150400-43154800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:43150600-43151800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:43150600-43151800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:43150600-43152200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:43150600-43152200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:43150600-43152800	Enhancers	HSMMtube	muscle
31	chr12:43150800-43151800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:43150800-43152400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr12:43150800-43154800	Enhancers	Fetal Lung	lung
34	chr12:43151000-43152000	Enhancers	Fetal Kidney	kidney
35	chr12:43151000-43153400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:43151000-43153400	Enhancers	Brain Germinal Matrix	brain
37	chr12:43151200-43151800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:43151200-43151800	Flanking Active TSS	NH-A	brain
39	chr12:43151200-43155400	Weak transcription	GM12878-XiMat	blood
40	chr12:43151400-43153000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:43151600-43151800	Enhancers	A549	lung
42	chr12:43151600-43152200	Enhancers	Fetal Muscle Leg	muscle
43	chr12:43151600-43152600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr12:43151600-43152600	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr12:43151600-43152800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr12:43151600-43153000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:43151600-43153600	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr12:43151600-43153600	Weak transcription	Hela-S3	cervix

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