Variant report

Variant	rs55674449
Chromosome Location	chr3:48940875-48940876
allele	A/G
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	EGR1	chr3:48940680-48940907	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48939596..48941508-chr3:48956180..48958109,2	K562	blood:
2	chr3:48936002..48938254-chr3:48939829..48942585,3	K562	blood:
3	chr3:48936002..48938268-chr3:48938899..48942585,3	K562	blood:

Variant related genes	Relation type
SLC25A20	TF binding region
ENSG00000221883	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000178537	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10780033	0.83[ASN][1000 genomes]
rs11130176	0.83[ASN][1000 genomes]
rs1134591	0.88[ASN][1000 genomes]
rs11705737	0.88[ASN][1000 genomes]
rs11708022	0.83[ASN][1000 genomes]
rs11709246	0.83[ASN][1000 genomes]
rs11712982	0.90[ASN][1000 genomes]
rs11713694	0.85[ASN][1000 genomes]
rs11717978	0.93[ASN][1000 genomes]
rs11719457	0.93[ASN][1000 genomes]
rs11920534	0.90[ASN][1000 genomes]
rs11924597	0.90[ASN][1000 genomes]
rs13064911	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13072911	0.88[ASN][1000 genomes]
rs13073997	0.88[ASN][1000 genomes]
rs13076394	0.81[AFR][1000 genomes]
rs13086240	0.90[ASN][1000 genomes]
rs13087930	0.93[ASN][1000 genomes]
rs13090839	0.90[ASN][1000 genomes]
rs13094900	0.85[ASN][1000 genomes]
rs13315711	0.88[ASN][1000 genomes]
rs13316620	0.80[ASN][1000 genomes]
rs28642807	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34477108	0.93[ASN][1000 genomes]
rs34504524	0.85[ASN][1000 genomes]
rs34509487	0.93[ASN][1000 genomes]
rs4072859	0.85[ASN][1000 genomes]
rs4974078	0.81[ASN][1000 genomes]
rs4974079	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4974080	0.81[ASN][1000 genomes]
rs4974082	0.85[ASN][1000 genomes]
rs4974084	0.90[ASN][1000 genomes]
rs4974085	0.83[ASN][1000 genomes]
rs4974087	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs56318350	0.93[ASN][1000 genomes]
rs6414613	0.81[ASN][1000 genomes]
rs6446196	0.90[ASN][1000 genomes]
rs6446198	0.88[ASN][1000 genomes]
rs6446205	0.81[ASN][1000 genomes]
rs6446252	0.83[ASN][1000 genomes]
rs67060340	0.88[ASN][1000 genomes]
rs67332931	0.83[ASN][1000 genomes]
rs6781790	0.81[ASN][1000 genomes]
rs6786665	0.88[ASN][1000 genomes]
rs6791234	0.88[ASN][1000 genomes]
rs71324924	0.83[ASN][1000 genomes]
rs7373778	0.85[ASN][1000 genomes]
rs7430198	0.93[ASN][1000 genomes]
rs7430501	0.83[ASN][1000 genomes]
rs7431710	0.88[ASN][1000 genomes]
rs7431857	0.83[ASN][1000 genomes]
rs7612459	0.83[ASN][1000 genomes]
rs7623023	0.83[ASN][1000 genomes]
rs7627404	0.80[ASN][1000 genomes]
rs7628719	0.88[ASN][1000 genomes]
rs7639332	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7643368	0.88[ASN][1000 genomes]
rs7649458	0.83[ASN][1000 genomes]
rs9311430	0.83[ASN][1000 genomes]
rs9311432	0.83[ASN][1000 genomes]
rs9311433	0.83[ASN][1000 genomes]
rs9681717	0.88[ASN][1000 genomes]
rs9682444	0.85[ASN][1000 genomes]
rs9754878	0.85[ASN][1000 genomes]
rs9755490	0.88[ASN][1000 genomes]
rs9830636	0.83[ASN][1000 genomes]
rs9835307	0.88[ASN][1000 genomes]
rs9840684	0.83[ASN][1000 genomes]
rs9850134	0.88[ASN][1000 genomes]
rs9867373	0.88[ASN][1000 genomes]
rs9876848	0.83[ASN][1000 genomes]
rs9879971	0.83[ASN][1000 genomes]
rs9884022	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv980012	chr3:48935037-48963512	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs55674449	WDR6	cis	brain	BrainEAC
rs55674449	WDR6	cis	Whole Blood	GTEx
rs55674449	WDR6	cis	lung	GTEx
rs55674449	WDR6	cis	Esophagus Mucosa	GTEx
rs55674449	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs55674449	CCDC36	cis	Esophagus Muscularis	GTEx
rs55674449	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48936600-48954800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:48936600-48954800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:48936800-48941200	Weak transcription	Placenta	Placenta
4	chr3:48936800-48948600	Weak transcription	Right Atrium	heart
5	chr3:48937200-48941000	Weak transcription	GM12878-XiMat	blood
6	chr3:48937200-48941000	Weak transcription	Hela-S3	cervix
7	chr3:48937200-48941000	Weak transcription	K562	blood
8	chr3:48937400-48941600	Weak transcription	Fetal Thymus	thymus
9	chr3:48937800-48941800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:48938000-48941000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:48938000-48941600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:48939800-48942600	Enhancers	Primary B cells from peripheral blood	blood
13	chr3:48940600-48941200	Enhancers	Primary B cells from cord blood	blood
14	chr3:48940600-48941200	Enhancers	Liver	Liver
15	chr3:48940600-48941200	Active TSS	HepG2	liver

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