Variant report

Variant	rs4529181
Chromosome Location	chr5:147468971-147468972
allele	C/G
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	MAFK	chr5:147468901-147469142	HepG2	liver:	n/a	chr5:147469006-147469017
2	ZKSCAN1	chr5:147468668-147469233	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:147468942-147468987	MCF10A-Er-Src	breast:	n/a	n/a
4	MAFK	chr5:147468822-147469281	Hela-S3	cervix:	n/a	chr5:147469244-147469254 chr5:147469006-147469017
5	RFX5	chr5:147468763-147470934	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
SPINK5	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10038561	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059850	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060214	0.83[EUR][1000 genomes]
rs10065129	0.86[EUR][1000 genomes]
rs10069070	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10073775	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1007977	0.83[EUR][1000 genomes]
rs1007978	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1017222	0.92[CEU][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs10213857	0.80[EUR][1000 genomes]
rs12108690	0.92[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs12514503	0.81[CEU][hapmap]
rs12519144	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12521761	0.83[EUR][1000 genomes]
rs1363729	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1422992	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs1422995	0.85[EUR][1000 genomes]
rs1422996	0.87[EUR][1000 genomes]
rs1423000	0.92[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs1423001	0.92[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs1423002	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1423003	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1423004	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1423005	0.83[EUR][1000 genomes]
rs1423006	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1423007	0.92[CEU][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.82[EUR][1000 genomes]
rs1609851	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1833768	0.83[EUR][1000 genomes]
rs1862439	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1862445	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1862446	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs2287772	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3752676	0.92[CEU][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs3756688	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs3777140	0.82[CEU][hapmap]
rs3777143	0.82[CEU][hapmap]
rs3815735	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs3815737	0.80[CEU][hapmap]
rs3822744	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4333302	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4357026	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4472254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4510567	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519912	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4610447	0.85[EUR][1000 genomes]
rs4705223	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs62388364	0.85[EUR][1000 genomes]
rs6580517	0.87[EUR][1000 genomes]
rs6580518	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580519	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580520	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6864564	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864920	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6876628	0.85[EUR][1000 genomes]
rs6889688	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894384	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7445392	0.81[CEU][hapmap]
rs7707841	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9325061	0.92[CEU][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs9325064	0.92[CEU][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs9325066	0.83[EUR][1000 genomes]
rs9325068	0.82[EUR][1000 genomes]
rs9325069	0.85[EUR][1000 genomes]
rs986493	0.83[EUR][1000 genomes]
rs986494	0.82[LWK][hapmap];0.81[MKK][hapmap]
rs986495	0.83[EUR][1000 genomes]
rs988885	0.82[CEU][hapmap];0.81[TSI][hapmap]

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	nsv1033838	chr5:147360521-147484014	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv933225	chr5:147395849-147486560	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4529181	SPINK5	cis	Adipose Subcutaneous	GTEx
rs4529181	SPINK5	cis	Thyroid	GTEx
rs4529181	SPINK5	cis	Heart Left Ventricle	GTEx
rs4529181	SPINK5	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147450400-147469000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:147450800-147474000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:147451000-147470000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:147454000-147470000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:147455600-147469000	Weak transcription	Esophagus	oesophagus
6	chr5:147462600-147471600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:147464000-147469800	Enhancers	Hela-S3	cervix
8	chr5:147464200-147491200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:147464400-147469800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:147464400-147488800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:147465600-147469000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:147466200-147469600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:147466200-147471600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:147467200-147469600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:147467200-147469600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:147467200-147469600	Weak transcription	NHEK	skin
17	chr5:147468200-147469000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:147468600-147469000	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:147468600-147471000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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