Variant report

Variant	rs16877662
Chromosome Location	chr5:79548274-79548275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79477424..79481349-chr5:79546234..79548720,3	MCF-7	breast:
2	chr5:79533016..79538413-chr5:79547668..79554494,9	MCF-7	breast:
3	chr5:79521252..79524016-chr5:79546932..79549730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239159	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2013057	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2112153	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2161094	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56893522	0.82[AFR][1000 genomes]
rs58850634	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59297647	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881707	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881708	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881709	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79541200-79548600	Enhancers	Liver	Liver
2	chr5:79542400-79550400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:79543600-79548400	Weak transcription	Fetal Brain Male	brain
4	chr5:79543600-79549000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:79543600-79549000	Weak transcription	Fetal Stomach	stomach
6	chr5:79543600-79549200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:79543600-79549200	Weak transcription	Ovary	ovary
8	chr5:79543600-79550600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:79543800-79548400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:79543800-79549000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:79543800-79549000	Weak transcription	Left Ventricle	heart
12	chr5:79543800-79549000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:79543800-79549200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:79543800-79549400	Weak transcription	Spleen	Spleen
15	chr5:79543800-79549800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:79544000-79548800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:79544000-79549000	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:79544200-79549000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:79544200-79549000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:79544200-79549000	Weak transcription	Right Atrium	heart
21	chr5:79544200-79549200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:79544200-79549400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:79544200-79550200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:79544200-79550400	Weak transcription	HSMM	muscle
25	chr5:79544200-79550600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:79544400-79548800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:79544400-79548800	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:79544400-79549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:79544400-79550000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:79544400-79550600	Weak transcription	Hela-S3	cervix
31	chr5:79544600-79549200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:79544600-79549800	Weak transcription	Primary B cells from cord blood	blood
33	chr5:79544600-79549800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:79544600-79550400	Weak transcription	HSMMtube	muscle
35	chr5:79544800-79548800	Weak transcription	NH-A	brain
36	chr5:79544800-79549000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr5:79544800-79549400	Weak transcription	K562	blood
38	chr5:79544800-79550400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:79544800-79550400	Weak transcription	GM12878-XiMat	blood
40	chr5:79545800-79548800	Enhancers	Brain Anterior Caudate	brain
41	chr5:79545800-79549000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr5:79545800-79549000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr5:79545800-79549000	Enhancers	Brain Cingulate Gyrus	brain
44	chr5:79545800-79549000	Enhancers	Brain Substantia Nigra	brain
45	chr5:79545800-79549000	Enhancers	Small Intestine	intestine
46	chr5:79546000-79548800	Enhancers	Brain Hippocampus Middle	brain
47	chr5:79546000-79550400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:79546200-79548800	Enhancers	Fetal Intestine Large	intestine
49	chr5:79546200-79549000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:79546400-79548800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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