Variant report

Variant	rs2555716
Chromosome Location	chr8:125937406-125937407
allele	C/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:125566501..125569219-chr8:125936752..125938690,2	MCF-7	breast:
2	chr8:125763544..125764471-chr8:125936648..125937472,2	MCF-7	breast:
3	chr8:125826307..125827972-chr8:125936472..125938461,2	MCF-7	breast:
4	chr8:125935909..125938271-chr8:125963994..125966987,3	MCF-7	breast:
5	chr8:125604579..125606037-chr8:125936216..125937900,23	MCF-7	breast:
6	chr8:125927702..125929777-chr8:125936123..125937814,2	MCF-7	breast:
7	chr8:125900652..125901659-chr8:125936406..125937477,4	MCF-7	breast:
8	chr8:125864651..125867984-chr8:125934838..125937619,3	MCF-7	breast:
9	chr8:125549812..125552337-chr8:125936366..125938525,2	MCF-7	breast:
10	chr8:125568500..125569404-chr8:125936057..125937539,6	MCF-7	breast:
11	chr8:125865723..125867850-chr8:125937365..125941183,3	MCF-7	breast:
12	chr8:125568422..125569389-chr8:125936437..125937567,3	MCF-7	breast:
13	chr8:125604990..125605930-chr8:125936492..125937604,6	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000255491	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000147684	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1317859	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs1427089	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2555721	0.80[EUR][1000 genomes]
rs7813655	0.82[YRI][hapmap]
rs7833872	0.82[YRI][hapmap]

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	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1030803	chr8:125868684-125969635	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1024405	chr8:125868684-125971035	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1020502	chr8:125868684-125972572	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2555716	MTSS1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125934400-125937600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr8:125935400-125937600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr8:125936400-125937600	Enhancers	Fetal Heart	heart
4	chr8:125936400-125937800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr8:125936600-125941200	Weak transcription	K562	blood
6	chr8:125936800-125937600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr8:125936800-125937600	Enhancers	Liver	Liver
8	chr8:125936800-125937600	Enhancers	Fetal Lung	lung
9	chr8:125936800-125937600	Enhancers	Right Atrium	heart
10	chr8:125937000-125937600	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr8:125937000-125938400	Enhancers	Left Ventricle	heart
12	chr8:125937200-125938200	Enhancers	Lung	lung
13	chr8:125937400-125938200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:125937400-125938600	Weak transcription	HMEC	breast
15	chr8:125937400-125939200	Weak transcription	Esophagus	oesophagus

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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

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