Variant report

Variant	rs12565977
Chromosome Location	chr1:70923537-70923538
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12561855	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12561944	0.83[ASN][1000 genomes]
rs12562375	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12562432	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12562754	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12564348	0.82[ASN][1000 genomes]
rs55952366	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57174209	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57922519	0.83[ASN][1000 genomes]
rs60589571	0.83[ASN][1000 genomes]
rs61704484	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6667807	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74085262	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74085263	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085264	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74085265	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74085266	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1002709	chr1:70916210-70939526	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70909000-70928200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:70917200-70925600	Weak transcription	NHDF-Ad	bronchial
3	chr1:70922800-70925800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:70923200-70924000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:70923200-70924200	Enhancers	Brain Substantia Nigra	brain
6	chr1:70923200-70924400	Enhancers	Brain Cingulate Gyrus	brain
7	chr1:70923200-70924600	Enhancers	Brain Hippocampus Middle	brain
8	chr1:70923200-70924800	Enhancers	Fetal Brain Male	brain
9	chr1:70923400-70923600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:70923400-70923800	Enhancers	Primary hematopoietic stem cells	blood
11	chr1:70923400-70923800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:70923400-70924400	Enhancers	Brain Anterior Caudate	brain
13	chr1:70923400-70924400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:70923400-70924800	Enhancers	Fetal Brain Female	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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