Variant report

Variant	rs290412
Chromosome Location	chr20:52702326-52702327
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:46672085..46674380-chr20:52701602..52704252,2	MCF-7	breast:
2	chr20:46612981..46615231-chr20:52699973..52702715,2	MCF-7	breast:
3	chr20:46419051..46422145-chr20:52700320..52703232,3	MCF-7	breast:
4	chr20:41010402..41013631-chr20:52701428..52704425,3	MCF-7	breast:
5	chr17:56734545..56738013-chr20:52696672..52702961,12	MCF-7	breast:
6	chr17:62229187..62231839-chr20:52701894..52704628,2	MCF-7	breast:
7	chr20:46475461..46477684-chr20:52701066..52703629,2	MCF-7	breast:
8	chr12:16502598..16504840-chr20:52700346..52703261,2	MCF-7	breast:
9	chr20:52701722..52703762-chr20:55824314..55825993,2	MCF-7	breast:
10	chr17:57913465..57916226-chr20:52700387..52703244,3	MCF-7	breast:
11	chr20:52701739..52704382-chr20:55838854..55841545,2	MCF-7	breast:
12	chr20:46412955..46417498-chr20:52699874..52705785,9	MCF-7	breast:
13	chr20:52701512..52703226-chr20:55844819..55846482,2	MCF-7	breast:
14	chr17:56707745..56710309-chr20:52697502..52703858,9	MCF-7	breast:
15	chr17:59710076..59712294-chr20:52701398..52703517,2	MCF-7	breast:
16	chr17:56735122..56737701-chr20:52700294..52703497,3	MCF-7	breast:
17	chr17:60003995..60006206-chr20:52702251..52704828,2	MCF-7	breast:
18	chr20:46412091..46416534-chr20:52700009..52706788,8	MCF-7	breast:
19	chr17:56703018..56712407-chr20:52697460..52725685,93	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction
ENSG00000108506	Chromatin interaction
ENSG00000008394	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4809951	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6022955	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127084	0.83[ASN][1000 genomes]
rs922376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928492	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928493	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52699200-52707000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr20:52700800-52702800	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr20:52700800-52703800	Enhancers	Stomach Mucosa	stomach
4	chr20:52701000-52706600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr20:52701200-52702400	Weak transcription	Gastric	stomach
6	chr20:52701200-52702600	Enhancers	HepG2	liver
7	chr20:52701200-52703000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr20:52701600-52702600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr20:52701600-52702800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:52701800-52703000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr20:52701800-52703200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr20:52701800-52703200	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr20:52701800-52703800	Enhancers	Adipose Nuclei	Adipose
14	chr20:52702000-52703800	Enhancers	A549	lung
15	chr20:52702200-52707600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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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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