Variant report

Variant	rs12780573
Chromosome Location	chr10:53779846-53779847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10733890	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11599067	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12243919	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12246992	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12570120	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12571078	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12780755	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4279961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4495849	0.95[EUR][1000 genomes]
rs7093536	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71508098	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7908149	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7921124	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2750961	chr10:53726294-54010594	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	nsv1040754	chr10:53758289-53845925	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv524814	chr10:53771085-53781507	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:53774800-53780400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:53778200-53781000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr10:53778400-53780200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:53778400-53781000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr10:53778400-53781200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr10:53778600-53781000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr10:53779000-53780000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr10:53779000-53790800	Weak transcription	Right Atrium	heart
9	chr10:53779200-53780000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:53779200-53780000	Weak transcription	Fetal Lung	lung
11	chr10:53779200-53780200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr10:53779200-53780400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:53779200-53780400	Weak transcription	Aorta	Aorta
14	chr10:53779200-53781000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr10:53779600-53780000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr10:53779600-53780600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr10:53779600-53781400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr10:53779800-53780200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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