Variant report

Variant	rs4536858
Chromosome Location	chr3:49193081-49193082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49192110..49194166-chr3:49199747..49201408,2	MCF-7	breast:
2	chr3:49191307..49193110-chr3:49202921..49204908,2	MCF-7	breast:
3	chr3:49189254..49193305-chr3:49194676..49199783,5	K562	blood:

Variant related genes	Relation type
ENSG00000270441	Chromatin interaction
ENSG00000177352	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10154895	0.97[ASN][1000 genomes]
rs10865954	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130182	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130184	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130185	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11552724	0.87[ASN][1000 genomes]
rs11706189	0.97[ASN][1000 genomes]
rs11712006	0.87[ASN][1000 genomes]
rs11713297	0.97[ASN][1000 genomes]
rs11715581	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716334	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717524	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11719220	0.81[ASN][1000 genomes]
rs11920267	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12487580	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490393	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493001	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629637	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12629759	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12631989	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12636030	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637576	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13064780	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13064784	0.82[ASN][1000 genomes]
rs13096406	0.89[ASN][1000 genomes]
rs2117938	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2334958	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3212	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34326553	0.87[ASN][1000 genomes]
rs34580506	0.87[ASN][1000 genomes]
rs34889065	0.87[ASN][1000 genomes]
rs35174559	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35218722	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35283189	0.87[ASN][1000 genomes]
rs35673421	0.87[ASN][1000 genomes]
rs4279134	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4308307	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4364202	0.80[ASN][1000 genomes]
rs4367098	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4499638	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513485	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4521268	0.82[ASN][1000 genomes]
rs4955410	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955418	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955419	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955420	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955432	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5030795	0.87[ASN][1000 genomes]
rs55713230	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61583136	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62262517	0.80[ASN][1000 genomes]
rs66991555	0.87[ASN][1000 genomes]
rs6770112	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6779394	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6784111	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6790914	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794924	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6795756	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7626445	0.82[ASN][1000 genomes]
rs7638154	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7645551	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7652746	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9814987	0.92[ASN][1000 genomes]
rs9835439	0.92[ASN][1000 genomes]
rs9837237	0.95[ASN][1000 genomes]
rs9837625	0.95[ASN][1000 genomes]
rs9840050	0.82[ASN][1000 genomes]
rs9855123	0.92[ASN][1000 genomes]
rs9862483	0.97[ASN][1000 genomes]
rs9880088	0.97[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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv3394931	chr3:49189548-49193146	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs4536858	NICN1	cis	Thyroid	GTEx
rs4536858	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4536858	WDR6	cis	Nerve Tibial	GTEx
rs4536858	WDR6	cis	Artery Tibial	GTEx
rs4536858	WDR6	cis	Whole Blood	GTEx
rs4536858	AMT	cis	Thyroid	GTEx
rs4536858	CCDC36	cis	Artery Tibial	GTEx
rs4536858	WDR6	cis	Heart Left Ventricle	GTEx
rs4536858	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4536858	WDR6	cis	lung	GTEx
rs4536858	WDR6	cis	Muscle Skeletal	GTEx
rs4536858	CCDC36	cis	Esophagus Muscularis	GTEx
rs4536858	NICN1-AS1	cis	Thyroid	GTEx
rs4536858	ARIH2	cis	Thyroid	GTEx
rs4536858	WDR6	cis	Esophagus Muscularis	GTEx
rs4536858	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4536858	AMT	cis	Muscle Skeletal	GTEx
rs4536858	NCKIPSD	cis	Esophagus Mucosa	GTEx
rs4536858	AMT	cis	Whole Blood	GTEx
rs4536858	AMT	cis	Artery Aorta	GTEx
rs4536858	NCKIPSD	cis	Muscle Skeletal	GTEx
rs4536858	WDR6	cis	Adipose Subcutaneous	GTEx
rs4536858	WDR6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:49186200-49198800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:49186800-49198800	Weak transcription	Pancreas	Pancrea
4	chr3:49190000-49195400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:49191000-49198800	Weak transcription	Ovary	ovary
6	chr3:49191000-49199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:49191400-49198800	Weak transcription	Gastric	stomach
8	chr3:49191400-49199000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:49191600-49200200	Weak transcription	Esophagus	oesophagus
10	chr3:49192000-49198000	Weak transcription	Thymus	Thymus
11	chr3:49192200-49198600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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