Variant report

Variant	rs10506215
Chromosome Location	chr12:43128894-43128895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:43127913..43130522-chr12:43133841..43135557,2	MCF-7	breast:
2	chr12:43128007..43129879-chr12:43150187..43151770,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1000413	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10128809	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10161278	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10785374	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10785375	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10785376	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10880360	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11181669	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12425497	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12578732	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12816928	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12830101	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2056195	0.84[EUR][1000 genomes]
rs3921403	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768445	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768446	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768447	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7310956	0.87[AMR][1000 genomes];0.97[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	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
rs10506215	NELL2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43119600-43130000	Weak transcription	Esophagus	oesophagus
2	chr12:43124200-43129200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:43124200-43129600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:43124400-43129400	Weak transcription	Fetal Stomach	stomach
5	chr12:43124400-43129800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:43124600-43129800	Weak transcription	HMEC	breast
7	chr12:43127000-43131800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr12:43127200-43130200	Enhancers	Fetal Heart	heart
9	chr12:43127400-43129600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:43127400-43129800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:43127400-43129800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:43128200-43130000	Enhancers	Fetal Muscle Leg	muscle
13	chr12:43128200-43130400	Enhancers	HSMMtube	muscle
14	chr12:43128400-43129200	Enhancers	Fetal Thymus	thymus
15	chr12:43128400-43129200	Enhancers	Right Atrium	heart
16	chr12:43128400-43129200	Enhancers	Right Ventricle	heart
17	chr12:43128400-43131800	Enhancers	Fetal Lung	lung
18	chr12:43128600-43129800	Weak transcription	Left Ventricle	heart
19	chr12:43128600-43129800	Enhancers	Stomach Smooth Muscle	stomach
20	chr12:43128600-43130000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:43128800-43129400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:43128800-43129800	Weak transcription	Psoas Muscle	Psoas
23	chr12:43128800-43130000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:43128800-43130200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr12:43128800-43131800	Enhancers	Colon Smooth Muscle	Colon

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