Variant report

Variant	rs12631548
Chromosome Location	chr3:56035991-56035992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1458060	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1458061	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17056288	0.87[EUR][1000 genomes]
rs17216524	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17825124	0.95[EUR][1000 genomes]
rs4974160	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57141558	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6779691	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6797314	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6805331	0.82[EUR][1000 genomes]
rs73086924	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73089182	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56033000-56037000	Weak transcription	Ovary	ovary
2	chr3:56033000-56052000	Weak transcription	Brain Germinal Matrix	brain
3	chr3:56033200-56046800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:56034600-56037200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:56034600-56037400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr3:56034800-56037800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:56035200-56037400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:56035400-56036600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:56035400-56040600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:56035600-56036400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:56035600-56036600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr3:56035600-56036600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:56035600-56037200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr3:56035800-56036000	Weak transcription	Fetal Kidney	kidney
15	chr3:56035800-56036200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:56035800-56036200	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr3:56035800-56036400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:56035800-56039200	Weak transcription	NH-A	brain

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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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