Variant report

Variant	rs12909643
Chromosome Location	chr15:53496468-53496469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11070963	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630091	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12907221	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12909492	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912144	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1354962	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1508022	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1567228	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774651	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774652	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774656	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774658	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs969908	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343986	chr15:53284440-53571936	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1037630	chr15:53324645-53708925	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1051634	chr15:53459129-53565627	Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3385784	chr15:53492461-53521900	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53493200-53497200	Enhancers	Dnd41	blood
2	chr15:53493400-53496800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr15:53493400-53497000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:53493800-53496600	Enhancers	Fetal Thymus	thymus
5	chr15:53493800-53496600	Enhancers	Thymus	Thymus
6	chr15:53493800-53497400	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:53495000-53498800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:53495200-53496600	Enhancers	Psoas Muscle	Psoas
9	chr15:53495200-53503000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:53495800-53496600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:53495800-53496600	Enhancers	HepG2	liver
12	chr15:53496000-53496600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr15:53496000-53500800	Weak transcription	Liver	Liver
14	chr15:53496200-53497000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:53496200-53497200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr15:53496400-53496600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:53496400-53497400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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