Variant report

Variant	rs10454909
Chromosome Location	chr5:88716714-88716715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1358555	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16867576	0.84[EUR][1000 genomes]
rs17508283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2161203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58661106	0.87[EUR][1000 genomes]
rs66580221	0.84[EUR][1000 genomes]
rs6891794	0.84[EUR][1000 genomes]
rs7701188	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532159	chr5:88016214-88783092	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv533373	chr5:88062497-89028098	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv529543	chr5:88348147-88783092	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv830388	chr5:88578939-88793870	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv598927	chr5:88647766-88780868	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
6	nsv830389	chr5:88669984-88860383	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv882357	chr5:88677293-88774328	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
8	nsv882358	chr5:88677293-88776034	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
9	nsv882359	chr5:88710519-88785384	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
10	nsv882360	chr5:88716714-88785384	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10454909	TMEM161B	cis	parietal	SCAN
rs10454909	NBPF22P	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:88713400-88717600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr5:88715000-88717000	Weak transcription	K562	blood
3	chr5:88715400-88717600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr5:88715600-88717200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:88715800-88717200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:88715800-88717200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr5:88715800-88717200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:88716200-88716800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:88716400-88717000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr5:88716400-88717400	Enhancers	Primary B cells from cord blood	blood
11	chr5:88716400-88717400	Enhancers	HUVEC	blood vessel
12	chr5:88716400-88717600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr5:88716400-88717600	Enhancers	Fetal Intestine Small	intestine
14	chr5:88716400-88717600	Enhancers	Hela-S3	cervix
15	chr5:88716600-88717200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:88716600-88717400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:88716600-88717400	Weak transcription	Fetal Intestine Large	intestine
18	chr5:88716600-88717400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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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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