Variant report

Variant	rs10154895
Chromosome Location	chr3:49174356-49174357
allele	G/T
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	POLR2A	chr3:49173817-49174359	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49172982..49175311-chr3:49207872..49210100,2	MCF-7	breast:
2	chr3:49164089..49168362-chr3:49172430..49175644,4	K562	blood:
3	chr3:49169871..49171871-chr3:49171986..49174689,3	K562	blood:
4	chr3:49173300..49174828-chr3:49194938..49196550,2	K562	blood:

Variant related genes	Relation type
LAMB2	TF binding region
ENSG00000185909	Chromatin interaction
ENSG00000172037	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10049462	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10865954	0.89[ASN][1000 genomes]
rs11130182	0.88[ASN][1000 genomes]
rs11130184	0.87[ASN][1000 genomes]
rs11552724	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11706052	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706189	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710247	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11712006	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11713297	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715581	0.92[ASN][1000 genomes]
rs11716334	0.87[ASN][1000 genomes]
rs11718982	0.89[EUR][1000 genomes]
rs11719220	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11719457	0.82[EUR][1000 genomes]
rs11720460	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12487580	0.90[ASN][1000 genomes]
rs12490393	0.92[ASN][1000 genomes]
rs12493001	1.00[ASN][1000 genomes]
rs12629759	0.87[ASN][1000 genomes]
rs12636030	1.00[ASN][1000 genomes]
rs12637576	0.87[ASN][1000 genomes]
rs12715434	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13064784	0.85[ASN][1000 genomes]
rs13068038	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13072554	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077498	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13080725	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086240	0.82[EUR][1000 genomes]
rs13087930	0.82[EUR][1000 genomes]
rs13090839	0.82[EUR][1000 genomes]
rs13096406	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28690891	0.81[AFR][1000 genomes]
rs3212	0.85[ASN][1000 genomes]
rs34326553	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34343820	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34504524	0.84[EUR][1000 genomes]
rs34509487	0.82[EUR][1000 genomes]
rs34566463	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34580506	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34784192	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34889065	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35060561	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35102816	0.84[EUR][1000 genomes]
rs35108630	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35185152	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35283189	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35673421	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3923475	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279134	0.85[ASN][1000 genomes]
rs4308307	0.92[ASN][1000 genomes]
rs4364202	0.83[ASN][1000 genomes]
rs4499638	0.97[ASN][1000 genomes]
rs4513485	0.85[ASN][1000 genomes]
rs4521268	0.85[ASN][1000 genomes]
rs4536858	0.97[ASN][1000 genomes]
rs4955410	0.95[ASN][1000 genomes]
rs4955418	0.97[ASN][1000 genomes]
rs4955419	0.92[ASN][1000 genomes]
rs4955420	0.92[ASN][1000 genomes]
rs5030795	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55713230	0.97[ASN][1000 genomes]
rs56306491	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56318350	0.82[EUR][1000 genomes]
rs61583136	0.95[ASN][1000 genomes]
rs61729488	0.80[EUR][1000 genomes]
rs62262517	0.83[ASN][1000 genomes]
rs66991555	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67286839	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6770112	0.95[ASN][1000 genomes]
rs6779394	0.89[ASN][1000 genomes]
rs67831908	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6784111	1.00[ASN][1000 genomes]
rs6790914	0.97[ASN][1000 genomes]
rs6794924	0.87[ASN][1000 genomes]
rs6795025	0.81[ASN][1000 genomes]
rs71324929	0.80[EUR][1000 genomes]
rs71324939	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73084135	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7615235	0.82[ASN][1000 genomes]
rs7626445	0.85[ASN][1000 genomes]
rs9311439	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9814987	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826525	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9828310	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9835439	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837237	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837625	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840050	0.85[ASN][1000 genomes]
rs9847839	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9850917	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9855123	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9862483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880309	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9990153	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10154895	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs10154895	WDR6	cis	Whole Blood	GTEx
rs10154895	WDR6	cis	Esophagus Mucosa	GTEx
rs10154895	WDR6	cis	Artery Tibial	GTEx
rs10154895	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49171600-49177000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:49171600-49178800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:49171600-49179000	Weak transcription	Thymus	Thymus
4	chr3:49172000-49177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:49172400-49175000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:49172400-49177400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:49172400-49177400	Weak transcription	Spleen	Spleen
9	chr3:49172800-49175400	Weak transcription	Pancreas	Pancrea
10	chr3:49172800-49177400	Weak transcription	Esophagus	oesophagus
11	chr3:49173000-49175000	Weak transcription	Placenta	Placenta
12	chr3:49173000-49177200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:49173200-49178800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:49173800-49175200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:49174000-49174800	Weak transcription	HepG2	liver
16	chr3:49174000-49179200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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