Variant report

Variant	rs59239860
Chromosome Location	chr1:154492107-154492108
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	STAT1	chr1:154492033-154492711	Hela-S3	cervix:	n/a	chr1:154492341-154492361 chr1:154492347-154492356 chr1:154492345-154492356 chr1:154492347-154492355 chr1:154492106-154492114 chr1:154492346-154492355
2	GATA1	chr1:154491907-154492527	PBDE	blood:	n/a	chr1:154492108-154492118
3	TFAP2C	chr1:154492027-154492555	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:154491965-154492635	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr1:154491840-154492659	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154485129..154487002-chr1:154490583..154492978,2	K562	blood:
2	chr1:154486201..154488615-chr1:154490445..154492712,2	MCF-7	breast:

Variant related genes	Relation type
TDRD10	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10047079	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11490956	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403537	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405637	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406822	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408461	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2229238	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3811448	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811449	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4072391	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41269915	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41308419	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41313910	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4379670	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4390168	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4633282	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4639752	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57783436	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58348886	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58710275	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58881140	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59084843	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59741504	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59838898	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60092776	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60255122	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60368585	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60498985	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60760897	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60931472	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61275241	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61403567	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61559765	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61698846	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669229	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6672087	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674171	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681207	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72999415	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72999419	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72999422	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73018293	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73020232	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73020234	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73020246	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73023331	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73023339	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73023346	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73023348	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73023349	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514452	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7526293	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7551873	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556449	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	esv1822921	chr1:154474131-154495697	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59239860	TDRD10	cis	lung	GTEx
rs59239860	TDRD10	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154488600-154497400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:154491800-154493000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:154491800-154493000	Enhancers	NHEK	skin
4	chr1:154491800-154493200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:154492000-154492200	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:154492000-154492600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:154492000-154492600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:154492000-154492600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:154492000-154492600	Enhancers	Fetal Heart	heart
10	chr1:154492000-154492600	Flanking Active TSS	Hela-S3	cervix
11	chr1:154492000-154493800	Enhancers	Left Ventricle	heart
12	chr1:154492000-154493800	Enhancers	Right Atrium	heart
13	chr1:154492000-154494000	Enhancers	Placenta	Placenta
14	chr1:154492000-154494800	Enhancers	Adipose Nuclei	Adipose
15	chr1:154492000-154494800	Enhancers	Right Ventricle	heart
16	chr1:154492000-154495200	Enhancers	Lung	lung

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