Variant report

Variant	rs12039980
Chromosome Location	chr1:85750432-85750433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85741905..85744580-chr1:85747619..85751624,6	K562	blood:
2	chr1:85742187..85745018-chr1:85749555..85753087,3	K562	blood:

Variant related genes	Relation type
ENSG00000223653	Chromatin interaction
ENSG00000142867	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11161566	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11161569	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11161572	0.84[ASN][1000 genomes]
rs11370	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12025860	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12025898	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12036224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12133263	0.83[ASN][1000 genomes]
rs12143319	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2735595	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768234	0.94[ASN][1000 genomes]
rs3768235	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85742800-85763000	Weak transcription	Ovary	ovary
2	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
3	chr1:85743200-85752000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:85745200-85753600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:85746800-85753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:85748600-85764000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:85748800-85750800	Enhancers	Esophagus	oesophagus
8	chr1:85749600-85755000	Weak transcription	A549	lung
9	chr1:85749800-85753000	Weak transcription	HMEC	breast
10	chr1:85749800-85755000	Weak transcription	Hela-S3	cervix
11	chr1:85749800-85755400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:85750000-85752800	Weak transcription	NHEK	skin
13	chr1:85750000-85753800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:85750000-85761400	Weak transcription	Lung	lung
15	chr1:85750000-85762800	Weak transcription	Pancreas	Pancrea
16	chr1:85750200-85750800	Strong transcription	Primary B cells from cord blood	blood
17	chr1:85750200-85751000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:85750200-85751000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:85750200-85751000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:85750200-85753800	Weak transcription	Stomach Mucosa	stomach
21	chr1:85750400-85750600	Bivalent Enhancer	HepG2	liver
22	chr1:85750400-85754200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:85750400-85762800	Weak transcription	Fetal Intestine Small	intestine

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