Variant report

Variant	rs2016802
Chromosome Location	chr5:116770509-116770510
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1030461	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1366185	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1366187	0.81[AMR][1000 genomes]
rs2245249	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2263587	0.82[AMR][1000 genomes]
rs2560583	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2560586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2560600	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2624463	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2624465	0.82[EUR][1000 genomes]
rs2624558	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830457	chr5:116724777-116875060	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv599487	chr5:116732456-116772093	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2016802	COMMD10	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116769000-116772200	Enhancers	Colon Smooth Muscle	Colon
2	chr5:116769400-116770600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr5:116769400-116770600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr5:116769400-116770800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:116769400-116770800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:116769400-116770800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr5:116769400-116771000	Enhancers	HSMMtube	muscle
8	chr5:116769400-116772400	Enhancers	Rectal Smooth Muscle	rectum
9	chr5:116769600-116770600	Enhancers	Stomach Smooth Muscle	stomach
10	chr5:116769600-116770800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr5:116769600-116770800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:116769600-116770800	Enhancers	Fetal Lung	lung
13	chr5:116770000-116771000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:116770200-116773000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:116770400-116770800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:116770400-116772800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:116770400-116773600	Weak transcription	ES-UCSF4 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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