Variant report

Variant	rs12153189
Chromosome Location	chr5:45109961-45109962
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12055286	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12153053	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12514414	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12516488	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12520430	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1472584	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4267876	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4308490	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4357042	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4493682	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4533895	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4566805	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56699889	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62367468	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62367469	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62367470	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62367473	0.85[EUR][1000 genomes]
rs62369894	0.90[AMR][1000 genomes]
rs62369895	0.90[AMR][1000 genomes]
rs62369896	0.90[AMR][1000 genomes]
rs62369905	0.80[ASN][1000 genomes]
rs62369907	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62369908	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62369910	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62369912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62369913	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62369916	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6898476	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7711444	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7711446	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7711528	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7720104	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033740	chr5:44996257-45378556	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv537743	chr5:44996257-45378556	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1018651	chr5:45003750-45437670	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv537744	chr5:45003750-45437670	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv869151	chr5:45003751-45362364	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv830280	chr5:45067773-45250757	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12153189	LOC647121	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:45108000-45110800	Weak transcription	Fetal Heart	heart
2	chr5:45109000-45110000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr5:45109200-45110000	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr5:45109200-45110200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:45109200-45113000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr5:45109200-45114400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr5:45109400-45110400	Enhancers	H9 Cell Line	embryonic stem cell
8	chr5:45109400-45110600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:45109400-45111600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:45109600-45110600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr5:45109600-45111200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:45109600-45111400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:45109800-45110000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:45109800-45110400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:45109800-45110400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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