Variant report

Variant	rs12090420
Chromosome Location	chr1:239811562-239811563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10925943	1.00[ASN][1000 genomes]
rs11807040	0.94[EUR][1000 genomes]
rs12057204	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063338	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070319	0.92[EUR][1000 genomes]
rs12090480	0.99[ASN][1000 genomes]
rs12094134	0.95[ASN][1000 genomes]
rs12097526	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16832153	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4465191	1.00[ASN][1000 genomes]
rs55873858	0.94[EUR][1000 genomes]
rs61836586	0.94[EUR][1000 genomes]
rs6429148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6657180	0.94[EUR][1000 genomes]
rs6691263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692904	0.99[ASN][1000 genomes]
rs6697471	0.94[EUR][1000 genomes]
rs6701925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726169	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs74150621	0.97[EUR][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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239797600-239811600	Weak transcription	Gastric	stomach
2	chr1:239807400-239811600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:239808600-239812400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:239808600-239813600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:239808600-239814800	Weak transcription	Pancreas	Pancrea
6	chr1:239808600-239818800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:239808800-239814600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:239810400-239812000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr1:239810800-239812000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:239811000-239811800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr1:239811000-239811800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:239811000-239812000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:239811000-239812000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:239811000-239812000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:239811200-239812000	Enhancers	Primary T cells from cord blood	blood
16	chr1:239811400-239811800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:239811400-239811800	Enhancers	Ovary	ovary
18	chr1:239811400-239811800	Enhancers	Spleen	Spleen
19	chr1:239811400-239812000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:239811400-239812000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr1:239811400-239812000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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