Variant report

Variant	rs7962745
Chromosome Location	chr12:43153849-43153850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11181672	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11181673	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11181674	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11181675	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11181676	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11181677	0.85[AMR][1000 genomes]
rs11181678	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11181679	0.91[CEU][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11181680	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11181681	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11181682	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12302566	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12313884	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1356421	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1356422	0.85[AMR][1000 genomes]
rs1356423	0.82[AMR][1000 genomes]
rs1914486	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1914487	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2203734	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2897590	0.94[ASW][hapmap];0.85[CEU][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs57284063	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs60367750	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61924560	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs61926694	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7963132	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7963276	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs868765	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs870972	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs955918	0.87[AFR][1000 genomes];0.83[AMR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7962745	NELL2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43149600-43154800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr12:43149600-43156400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:43149800-43154000	Enhancers	H9 Cell Line	embryonic stem cell
4	chr12:43149800-43155200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:43149800-43156600	Enhancers	HMEC	breast
6	chr12:43150200-43154000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr12:43150200-43154400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:43150200-43154400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr12:43150200-43155200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:43150400-43154800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:43150800-43154800	Enhancers	Fetal Lung	lung
12	chr12:43151200-43155400	Weak transcription	GM12878-XiMat	blood
13	chr12:43152000-43154600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:43152200-43154200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:43152200-43154600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:43152200-43155600	Weak transcription	HSMM	muscle
17	chr12:43152600-43154400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:43152600-43154800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr12:43152800-43154000	Enhancers	Psoas Muscle	Psoas
20	chr12:43152800-43155000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:43152800-43155400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr12:43153000-43156800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:43153200-43154800	Enhancers	Fetal Muscle Leg	muscle
24	chr12:43153200-43156600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:43153200-43156600	Enhancers	Osteobl	bone
26	chr12:43153400-43154600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:43153400-43154800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:43153400-43155000	Enhancers	Adipose Nuclei	Adipose
29	chr12:43153400-43156200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:43153600-43154400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:43153600-43154600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr12:43153600-43154600	Enhancers	Rectal Smooth Muscle	rectum
33	chr12:43153600-43154600	Enhancers	Stomach Smooth Muscle	stomach
34	chr12:43153600-43156000	Enhancers	Hela-S3	cervix
35	chr12:43153800-43154000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:43153800-43154200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:43153800-43154200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:43153800-43154600	Weak transcription	Ovary	ovary
39	chr12:43153800-43156600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:43153800-43161800	Weak transcription	Pancreas	Pancrea

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