Variant report

Variant	rs808042
Chromosome Location	chr5:103252374-103252375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1469456	0.87[ASN][1000 genomes]
rs246372	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs246381	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs712144	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs808043	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882523	chr5:102687151-103342745	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1025859	chr5:102744479-103710290	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537833	chr5:102744479-103710290	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv599195	chr5:102982978-103296777	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830432	chr5:103088161-103280243	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv462326	chr5:103225174-103254427	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv599197	chr5:103225174-103254427	Weak transcription Enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv462327	chr5:103228629-103258936	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv599198	chr5:103228629-103258936	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv882524	chr5:103237745-104019292	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv462329	chr5:103244640-103264987	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv599199	chr5:103244640-103264987	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv599200	chr5:103249714-103277997	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs808042	CMTM5	trans	parietal	SCAN
rs808042	C3orf26	trans	parietal	SCAN
rs808042	PAM	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:103245000-103254400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:103246400-103254000	Weak transcription	NH-A	brain
3	chr5:103248800-103254400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:103250600-103255400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:103251200-103254000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:103251200-103254000	Weak transcription	Osteobl	bone
7	chr5:103251200-103254200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:103251400-103253200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:103251800-103254000	Weak transcription	HSMMtube	muscle
10	chr5:103252200-103252400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr5:103252200-103252400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr5:103252200-103252600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr5:103252200-103252600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr5:103252200-103252600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:103252200-103252600	Enhancers	Brain Cingulate Gyrus	brain
16	chr5:103252200-103252800	Enhancers	Brain Hippocampus Middle	brain
17	chr5:103252200-103253000	Enhancers	Cortex derived primary cultured neurospheres	brain

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

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