Variant report

Variant	rs10464070
Chromosome Location	chr5:178055922-178055923
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	chr5:178055686-178056033	MCF10A-Er-Src	breast:	n/a	n/a
2	FOXA2	chr5:178055783-178056679	HepG2	liver:	n/a	n/a
3	FOXA1	chr5:178055855-178056381	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:178052987..178056050-chr5:178056072..178058258,3	MCF-7	breast:
2	chr5:178054261..178056030-chr5:178057503..178059124,2	MCF-7	breast:
3	chr5:178054847..178056678-chr5:178067285..178069085,2	K562	blood:
4	chr5:178054153..178056905-chr5:178057584..178060537,3	K562	blood:

Variant related genes	Relation type
CLK4	TF binding region
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10035569	0.88[ASN][1000 genomes]
rs10063148	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10066600	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10070146	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10070856	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10464049	0.88[ASN][1000 genomes]
rs10479431	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479500	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11747899	0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs12054903	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12188543	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12189095	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12234109	0.87[ASN][1000 genomes]
rs13181921	0.91[ASN][1000 genomes]
rs2045892	0.86[ASN][1000 genomes]
rs262023	0.85[ASN][1000 genomes]
rs262024	0.86[ASN][1000 genomes]
rs262029	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs262033	0.87[ASN][1000 genomes]
rs34183525	0.87[ASN][1000 genomes]
rs34724127	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34893037	0.87[ASN][1000 genomes]
rs35178365	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35604659	0.88[ASN][1000 genomes]
rs35943178	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3925517	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4424014	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4437395	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4579274	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4976738	0.82[CEU][hapmap]
rs543862	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs55724549	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55783860	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57862544	0.94[ASN][1000 genomes]
rs62392801	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6884172	0.93[ASN][1000 genomes]
rs6884657	0.93[ASN][1000 genomes]
rs71611451	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71611452	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7447517	0.86[ASN][1000 genomes]
rs7700943	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7724406	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9329047	0.86[EUR][1000 genomes];0.91[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10464070	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178054600-178057200	Enhancers	HepG2	liver
2	chr5:178054600-178057400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:178054600-178057400	Weak transcription	K562	blood
4	chr5:178054600-178057600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:178054600-178057800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:178054600-178058800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:178054600-178059200	Weak transcription	Right Atrium	heart
8	chr5:178054600-178061600	Weak transcription	HMEC	breast
9	chr5:178054800-178057200	Weak transcription	NHEK	skin
10	chr5:178054800-178057400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:178054800-178057400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:178054800-178057400	Weak transcription	Hela-S3	cervix
13	chr5:178054800-178057400	Weak transcription	NH-A	brain
14	chr5:178054800-178057400	Weak transcription	Osteobl	bone
15	chr5:178054800-178058000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:178055000-178057400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr5:178055000-178057800	Weak transcription	Primary B cells from cord blood	blood
18	chr5:178055200-178056000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr5:178055800-178056000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell

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