Variant report

Variant	rs290267
Chromosome Location	chr9:93552550-93552551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10993687	0.96[ASN][1000 genomes]
rs12682691	0.96[ASN][1000 genomes]
rs12685044	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1333639	0.92[ASN][1000 genomes]
rs1993703	0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs290269	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs291005	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748188	0.92[ASN][1000 genomes]
rs4744009	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4744013	0.92[ASN][1000 genomes]
rs4744498	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4744502	0.92[ASN][1000 genomes]
rs4744504	0.92[ASN][1000 genomes]
rs4744508	0.85[ASN][1000 genomes]
rs7868795	0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv893567	chr9:93519280-93609668	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv893569	chr9:93552550-93587089	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs290267	ITGAM	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93550000-93557400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:93550800-93552800	Enhancers	Primary B cells from peripheral blood	blood
3	chr9:93551400-93552600	Enhancers	Primary B cells from cord blood	blood
4	chr9:93551800-93552600	Enhancers	Placenta	Placenta
5	chr9:93551800-93552800	Enhancers	Fetal Stomach	stomach
6	chr9:93551800-93563400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:93552000-93552600	Enhancers	Fetal Kidney	kidney
8	chr9:93552000-93552800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:93552000-93563400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:93552200-93552600	Enhancers	Fetal Muscle Leg	muscle
11	chr9:93552400-93552600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr9:93552400-93552600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:93552400-93555600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr9:93552400-93556000	Weak transcription	Primary monocytes fromperipheralblood	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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