Variant report

Variant	rs11150610
Chromosome Location	chr16:31334236-31334237
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr16:31333590-31334309	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:31332982..31334824-chr16:31338109..31339685,2	MCF-7	breast:
2	chr16:31331494..31335412-chr16:31342610..31345111,3	K562	blood:
3	chr16:31200877..31205446-chr16:31331682..31336266,5	K562	blood:

Variant related genes	Relation type
ITGAM	TF binding region
ENSG00000089280	Chromatin interaction
ENSG00000169896	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10747210	0.86[ASN][1000 genomes]
rs10782004	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1106398	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11150608	0.90[EUR][1000 genomes]
rs11150611	0.87[ASN][1000 genomes]
rs11150612	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.89[ASN][1000 genomes]
rs11150613	0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11150614	0.86[CHB][hapmap]
rs11150616	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11150619	0.84[MEX][hapmap]
rs1143682	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11574630	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs11574631	0.93[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11641202	0.97[CHD][hapmap];0.97[ASN][1000 genomes]
rs11642120	0.92[ASN][1000 genomes]
rs11645917	0.88[ASN][1000 genomes]
rs11859274	0.88[ASN][1000 genomes]
rs11863627	0.96[ASN][1000 genomes]
rs12597154	0.88[ASN][1000 genomes]
rs12600286	0.82[ASN][1000 genomes]
rs12923297	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs12935192	0.88[ASN][1000 genomes]
rs13332545	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs13338928	0.97[ASN][1000 genomes]
rs2359661	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs28372932	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3087796	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs36100148	0.97[ASN][1000 genomes]
rs3815801	0.84[JPT][hapmap]
rs3925074	0.93[ASN][1000 genomes]
rs3925075	0.93[ASN][1000 genomes]
rs4075052	0.92[ASN][1000 genomes]
rs4077810	0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs41440449	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4261553	0.92[ASN][1000 genomes]
rs4359460	0.92[ASN][1000 genomes]
rs4411512	0.92[ASN][1000 genomes]
rs4448960	0.93[ASN][1000 genomes]
rs4450409	0.85[ASN][1000 genomes]
rs4459557	0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4493054	0.86[ASN][1000 genomes]
rs4506917	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4594268	0.92[ASN][1000 genomes]
rs4597342	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4608351	0.92[ASN][1000 genomes]
rs4889543	0.98[ASN][1000 genomes]
rs4889647	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889649	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs55742763	0.98[ASN][1000 genomes]
rs56392848	0.87[ASN][1000 genomes]
rs57202326	0.85[ASN][1000 genomes]
rs59338016	0.88[ASN][1000 genomes]
rs61194152	0.87[ASN][1000 genomes]
rs62051517	0.97[ASN][1000 genomes]
rs7192161	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7192375	0.97[ASN][1000 genomes]
rs7195915	0.97[ASN][1000 genomes]
rs7195945	0.97[ASN][1000 genomes]
rs7206295	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7499192	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7501207	0.83[ASN][1000 genomes]
rs8048583	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs8052324	0.97[ASN][1000 genomes]
rs8058882	0.87[ASN][1000 genomes]
rs8060268	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8062159	0.86[ASN][1000 genomes]
rs9673398	0.94[ASN][1000 genomes]
rs9673404	0.92[ASN][1000 genomes]
rs9673405	0.93[ASN][1000 genomes]
rs9673519	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9673522	0.93[ASN][1000 genomes]
rs9674009	0.93[ASN][1000 genomes]
rs9888907	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
2	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systemic lupus erythematosus	19165918	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11150610	ITGAX	cis	multi-tissue	Pritchard
rs11150610	TAOK2	cis	cerebellum	SCAN
rs11150610	TBX6	cis	parietal	SCAN
rs11150610	PYCARD	cis	lymphoblastoid	seeQTL
rs11150610	CCDC101	cis	parietal	SCAN
rs11150610	ITGAM	cis	cerebellum	SCAN
rs11150610	PRSS36	cis	parietal	SCAN
rs11150610	ITGAM	cis	lymphoblastoid	seeQTL
rs11150610	SULT1A2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31323000-31344600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr16:31331600-31334400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:31331800-31342000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr16:31332200-31342000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr16:31333400-31335200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
6	chr16:31333600-31339600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:31333600-31342400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr16:31333800-31342400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr16:31334000-31338200	Weak transcription	Primary B cells from cord blood	blood
10	chr16:31334200-31335600	Weak transcription	Spleen	Spleen

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