Variant report

Variant	rs1125823
Chromosome Location	chr3:45902963-45902964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1029732	0.80[ASN][1000 genomes]
rs11712469	0.94[ASN][1000 genomes]
rs13065964	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386930	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1488369	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2129880	0.95[ASN][1000 genomes]
rs7614952	0.80[ASN][1000 genomes]
rs7625839	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855780	0.82[AFR][1000 genomes];1.00[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45890000-45907400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:45891800-45905200	Weak transcription	Psoas Muscle	Psoas
3	chr3:45894600-45906200	Genic enhancers	Dnd41	blood
4	chr3:45901600-45904200	Enhancers	Fetal Intestine Large	intestine
5	chr3:45901600-45904200	Enhancers	Fetal Intestine Small	intestine
6	chr3:45902000-45903800	Enhancers	Fetal Thymus	thymus
7	chr3:45902200-45903200	Bivalent Enhancer	K562	blood
8	chr3:45902200-45903400	Enhancers	Primary T cells from cord blood	blood
9	chr3:45902200-45903600	Enhancers	Duodenum Mucosa	Duodenum
10	chr3:45902200-45903600	Flanking Active TSS	GM12878-XiMat	blood
11	chr3:45902400-45903200	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:45902400-45903200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr3:45902400-45903600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr3:45902600-45903200	Enhancers	Thymus	Thymus
15	chr3:45902600-45910200	Weak transcription	Gastric	stomach
16	chr3:45902800-45903200	Flanking Active TSS	Liver	Liver
17	chr3:45902800-45903600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:45902800-45906000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:45902800-45906400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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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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