Variant report

Variant	rs10925914
Chromosome Location	chr1:239711050-239711051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10754672	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10802774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10925908	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10925910	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10925911	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10925912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10925913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023414	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1416380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1416381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1899606	0.82[ASN][1000 genomes]
rs4659917	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239701400-239711800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:239702000-239711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:239710400-239711400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:239710600-239711200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr1:239710600-239711200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:239710600-239711600	Enhancers	Colon Smooth Muscle	Colon
7	chr1:239710600-239711800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:239710600-239712000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:239710800-239711200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:239710800-239711200	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr1:239710800-239720600	Weak transcription	Stomach Mucosa	stomach
12	chr1:239711000-239711200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr1:239711000-239711400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:239711000-239711800	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr1:239711000-239712000	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr1:239711000-239712000	Active TSS	Primary T helper naive cells fromperipheralblood	blood

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

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