Variant report

Variant	rs590843
Chromosome Location	chr11:119991166-119991167
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000110400	Chromatin interaction
ENSG00000176984	Chromatin interaction
ENSG00000137699	Chromatin interaction
ENSG00000254854	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs470392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs470941	0.86[CHB][hapmap]
rs530294	0.92[ASN][1000 genomes]
rs550164	0.86[CHB][hapmap]
rs670855	0.85[CHB][hapmap]

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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs590843	THY1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119981800-119991200	Strong transcription	HMEC	breast
2	chr11:119981800-119991400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr11:119985400-119993000	Weak transcription	Right Atrium	heart
4	chr11:119985800-119991200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:119987400-119994400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:119987800-119992200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:119988400-119992000	Weak transcription	Fetal Thymus	thymus
8	chr11:119989000-119991400	Strong transcription	NHEK	skin
9	chr11:119989200-119992400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:119989400-119992200	Genic enhancers	Esophagus	oesophagus
11	chr11:119989800-119991400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:119990000-119991200	Weak transcription	Hela-S3	cervix
13	chr11:119990200-119991600	Weak transcription	Spleen	Spleen
14	chr11:119990200-119992400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:119990400-119993000	Weak transcription	Gastric	stomach
16	chr11:119990600-119991200	Genic enhancers	Placenta	Placenta

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links