Variant report

Variant	rs10925920
Chromosome Location	chr1:239750780-239750781
allele	C/T
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:24)

rs_ID	r²[population]
rs10127769	0.97[ASN][1000 genomes]
rs10754674	0.97[ASN][1000 genomes]
rs10754675	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10802776	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10802777	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10802778	0.91[ASN][1000 genomes]
rs10802779	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10802780	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10925918	0.87[ASN][1000 genomes]
rs10925921	0.94[ASN][1000 genomes]
rs10925926	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12089818	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12118974	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12402224	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1416378	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1538442	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1867262	0.97[ASN][1000 genomes]
rs4376722	0.97[ASN][1000 genomes]
rs4507997	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4659547	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4659920	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7526165	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs997148	0.97[ASN][1000 genomes]
rs997538	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:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239728800-239769400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:239744000-239761400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:239746400-239756200	Weak transcription	Gastric	stomach
4	chr1:239746600-239757600	Weak transcription	Pancreas	Pancrea
5	chr1:239747000-239754600	Weak transcription	Fetal Kidney	kidney
6	chr1:239747400-239750800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:239747400-239753400	Weak transcription	Ovary	ovary
8	chr1:239748600-239751000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:239748600-239751000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:239750200-239750800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:239750200-239751000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:239750200-239751200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:239750400-239750800	Enhancers	Primary T cells from cord blood	blood
14	chr1:239750400-239750800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr1:239750400-239751000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:239750400-239751800	Enhancers	Colon Smooth Muscle	Colon
17	chr1:239750600-239753400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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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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