Variant report

Variant	rs10053496
Chromosome Location	chr5:167711228-167711229
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10052800	1.00[ASW][hapmap]
rs10058240	1.00[AMR][1000 genomes]
rs11950425	1.00[AMR][1000 genomes]
rs17070041	1.00[AMR][1000 genomes]
rs3886252	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs58247534	1.00[AMR][1000 genomes]
rs58728182	1.00[AMR][1000 genomes]
rs60173126	1.00[AMR][1000 genomes]
rs61687180	1.00[AMR][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	nsv534607	chr5:167661667-168454396	Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv5117	chr5:167666701-167711857	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv949154	chr5:167691208-168323234	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10053496	SYCE1	trans	lymphoblastoid	seeQTL
rs10053496	MIR650	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167704400-167713000	Weak transcription	Fetal Brain Male	brain
2	chr5:167704600-167718000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:167704800-167712400	Weak transcription	Gastric	stomach
4	chr5:167709400-167712800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:167709400-167713200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:167709600-167713000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:167709600-167713000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:167709600-167713000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:167709600-167713400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:167709600-167713600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:167709600-167714800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:167709600-167718000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:167709600-167718000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:167709600-167718000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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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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