Variant report

Variant	rs28405193
Chromosome Location	chr1:104678487-104678488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10449725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11576074	1.00[ASN][1000 genomes]
rs11577070	1.00[ASN][1000 genomes]
rs11583722	1.00[ASN][1000 genomes]
rs1928301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928315	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1932473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57106041	1.00[EUR][1000 genomes]
rs59789357	1.00[EUR][1000 genomes]
rs6671467	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6679346	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72685703	1.00[ASN][1000 genomes]
rs72685776	1.00[ASN][1000 genomes]
rs72685792	1.00[ASN][1000 genomes]
rs72685793	1.00[ASN][1000 genomes]
rs72685796	1.00[ASN][1000 genomes]
rs72689166	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689167	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689174	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689176	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689177	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689180	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689182	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689183	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689185	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689186	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689187	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs943962	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs943964	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014507	chr1:104307231-104784753	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012931	chr1:104322484-104778961	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872072	chr1:104470622-105076810	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1010903	chr1:104483363-105468941	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv872073	chr1:104502333-104719055	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1839044	chr1:104576359-104707906	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv482341	chr1:104589525-104731812	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3346122	chr1:104676790-104678604	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:104675600-104679200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:104676800-104679800	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr1:104678000-104679800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
4	chr1:104678000-104687000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:104678400-104678600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:104678400-104678600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:104678400-104678600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:104678400-104678800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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