Variant report

Variant	rs12413316
Chromosome Location	chr10:54623942-54623943
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12411673	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12412393	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12413880	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12415503	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16934429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934609	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36030089	0.92[ASN][1000 genomes]
rs4935365	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58548489	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73343239	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73343241	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73343242	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73343247	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73343252	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73343256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73343266	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73343272	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73345214	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7915776	0.99[ASN][1000 genomes]
rs7920685	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv831876	chr10:54492511-54649392	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv895404	chr10:54545590-54850707	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv831877	chr10:54565135-54764638	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv467200	chr10:54585401-54726056	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv550905	chr10:54585401-54726056	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1041940	chr10:54621342-54737528	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54622600-54625200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr10:54622600-54625200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:54622600-54625400	Enhancers	HMEC	breast
4	chr10:54623000-54625400	Enhancers	NHEK	skin
5	chr10:54623000-54626000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:54623200-54626000	Enhancers	NHLF	lung
7	chr10:54623400-54624600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:54623400-54625000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:54623400-54625200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:54623400-54625200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:54623400-54625400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:54623400-54625400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr10:54623600-54624600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr10:54623600-54624600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr10:54623600-54625000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr10:54623600-54625000	Enhancers	Fetal Intestine Large	intestine
17	chr10:54623600-54625200	Enhancers	NH-A	brain
18	chr10:54623800-54624000	Enhancers	HSMM	muscle
19	chr10:54623800-54624400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:54623800-54624600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr10:54623800-54624800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr10:54623800-54624800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr10:54623800-54624800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr10:54623800-54624800	Enhancers	Fetal Heart	heart
25	chr10:54623800-54624800	Enhancers	HepG2	liver
26	chr10:54623800-54624800	Enhancers	HSMMtube	muscle
27	chr10:54623800-54625000	Enhancers	Fetal Intestine Small	intestine
28	chr10:54623800-54625200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr10:54623800-54625200	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr10:54623800-54625200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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