Variant report

Variant	rs7539998
Chromosome Location	chr1:70001102-70001103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10889836	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10889837	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12045969	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12067577	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891221	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1935245	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6424551	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424552	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656228	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7528888	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7531225	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7540187	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7540901	0.83[ASN][1000 genomes]
rs7542641	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs912774	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949691	chr1:69749722-70302201	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3384194	chr1:69885024-70275430	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv436273	chr1:69996026-70002655	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3453318	chr1:69996377-70002707	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3453319	chr1:69996377-70002707	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv20770	chr1:69996393-70002209	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1809309	chr1:69996616-70001259	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv1812760	chr1:69996616-70001259	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv1805388	chr1:69996616-70019811	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1807543	chr1:69996616-70019811	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1809423	chr1:69996616-70019811	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1810945	chr1:69996616-70019811	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70000400-70001400	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr1:70000800-70001400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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