Variant report

Variant	rs61137521
Chromosome Location	chr3:48757773-48757774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48753321..48755795-chr3:48757352..48760937,4	MCF-7	breast:
2	chr3:48754717..48757980-chr3:48775781..48778989,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10865952	0.81[ASN][1000 genomes]
rs11557629	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706203	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11706983	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11708786	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11715177	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11719291	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12493578	0.81[ASN][1000 genomes]
rs12497850	0.81[ASN][1000 genomes]
rs13063223	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090013	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13316551	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13324950	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13434258	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1352420	0.81[ASN][1000 genomes]
rs17080319	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28567949	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28657585	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28793701	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34153629	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35064573	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4077495	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4858798	0.81[ASN][1000 genomes]
rs4858828	0.81[ASN][1000 genomes]
rs4858831	0.81[ASN][1000 genomes]
rs56735597	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6788650	0.81[ASN][1000 genomes]
rs9811027	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9834996	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848203	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9854034	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9877542	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9877685	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9882549	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs61137521	WDR6	cis	lung	GTEx
rs61137521	WDR6	cis	Whole Blood	GTEx
rs61137521	WDR6	cis	Esophagus Mucosa	GTEx
rs61137521	WDR6	cis	Artery Tibial	GTEx
rs61137521	WDR6	cis	Adipose Subcutaneous	GTEx
rs61137521	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs61137521	USP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48754800-48759000	Weak transcription	Gastric	stomach
2	chr3:48755200-48758000	Weak transcription	Fetal Lung	lung
3	chr3:48755200-48759000	Weak transcription	Fetal Kidney	kidney
4	chr3:48755200-48760000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:48755200-48760200	Weak transcription	Small Intestine	intestine
6	chr3:48755400-48758000	Weak transcription	Fetal Intestine Large	intestine
7	chr3:48755400-48758000	Weak transcription	Stomach Mucosa	stomach
8	chr3:48755400-48759000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:48755400-48760200	Weak transcription	Colonic Mucosa	Colon
10	chr3:48755400-48760200	Weak transcription	A549	lung
11	chr3:48755400-48760400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:48755600-48760200	Weak transcription	K562	blood
13	chr3:48756000-48759000	Weak transcription	Pancreas	Pancrea
14	chr3:48756200-48758800	Weak transcription	HepG2	liver
15	chr3:48756800-48758800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:48757000-48760000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr3:48757600-48757800	Enhancers	Spleen	Spleen
18	chr3:48757600-48758000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:48757600-48758200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:48757600-48758200	Enhancers	Fetal Intestine Small	intestine

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