Variant report

Variant	rs2120240
Chromosome Location	chr1:239808324-239808325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12021521	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12021774	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037424	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12039288	0.86[EUR][1000 genomes]
rs12042581	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16832150	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16832152	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28809572	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60744906	0.84[EUR][1000 genomes]
rs66475080	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713117	0.88[EUR][1000 genomes]
rs72758715	0.94[ASN][1000 genomes]
rs72758725	0.89[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2120240	EDARADD	cis	parietal	SCAN

Chromatin state (count:12 , 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	chr1:239806400-239808600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr1:239806800-239808800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:239806800-239809800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:239807200-239808600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:239807400-239809400	Weak transcription	Fetal Stomach	stomach
8	chr1:239807400-239811600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:239807600-239808600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:239808000-239808600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:239808200-239808600	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr1:239808200-239808600	ZNF genes & repeats	Pancreas	Pancrea

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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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