Variant report

Variant	rs7540053
Chromosome Location	chr1:239809723-239809724
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16838647	1.00[AFR][1000 genomes]
rs16838650	1.00[AFR][1000 genomes]
rs16838801	0.82[ASW][hapmap]
rs16842802	0.90[AFR][1000 genomes]
rs6672919	0.98[AFR][1000 genomes]
rs6677810	1.00[AFR][1000 genomes]
rs6692140	0.87[AFR][1000 genomes]
rs6692141	0.87[AFR][1000 genomes]
rs6699221	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6700941	0.98[AFR][1000 genomes]
rs7513450	1.00[AFR][1000 genomes]
rs7514567	0.94[AFR][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	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2757778	chr1:239766094-240389504	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv2759009	chr1:239766094-240389504	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv468628	chr1:239774670-239812103	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv468639	chr1:239774670-239812103	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv549438	chr1:239774670-239812103	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239797600-239811600	Weak transcription	Gastric	stomach
2	chr1:239804600-239811000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:239806800-239809800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:239807400-239811600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:239808600-239811000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:239808600-239811400	Weak transcription	Ovary	ovary
7	chr1:239808600-239812400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:239808600-239813600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:239808600-239814800	Weak transcription	Pancreas	Pancrea
10	chr1:239808600-239818800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:239808800-239814600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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