Variant report

Variant	rs6049339
Chromosome Location	chr20:24006684-24006685
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16986164	0.83[EUR][1000 genomes]
rs3848800	0.80[AMR][1000 genomes]
rs3848801	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3859656	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3905229	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6036616	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036617	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6036619	0.97[EUR][1000 genomes]
rs6036620	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049329	0.80[AMR][1000 genomes]
rs6049331	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6049332	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6049337	0.93[EUR][1000 genomes]
rs6049338	0.94[EUR][1000 genomes]
rs6049346	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049348	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6049352	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6114414	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6114418	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833944	chr20:23806288-24021865	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1063474	chr20:23918394-24048069	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1056491	chr20:23955040-24105080	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv585731	chr20:23989027-24024259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24003800-24008000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:24005600-24007400	Enhancers	Dnd41	blood
3	chr20:24005800-24008400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr20:24006000-24008000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr20:24006000-24008000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr20:24006000-24008200	Enhancers	Primary T cells from cord blood	blood
7	chr20:24006000-24008200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr20:24006000-24008200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr20:24006000-24008600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr20:24006000-24009200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr20:24006200-24007000	Enhancers	Primary hematopoietic stem cells	blood
12	chr20:24006200-24007400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr20:24006200-24007600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr20:24006200-24008200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr20:24006200-24009200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr20:24006200-24009200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr20:24006400-24009200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr20:24006600-24006800	Enhancers	Psoas Muscle	Psoas
19	chr20:24006600-24007600	Weak transcription	Small Intestine	intestine

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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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