Variant report

Variant	rs9596643
Chromosome Location	chr13:52912380-52912381
allele	A/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	FOXA1	chr13:52912110-52912661	HepG2	liver:	n/a	n/a
2	CTCF	chr13:52912320-52912470	HMEC	breast:	n/a	n/a
3	CTCF	chr13:52912360-52912510	HepG2	liver:	n/a	n/a
4	FOXA2	chr13:52912168-52912516	HepG2	liver:	n/a	n/a
5	FOXA1	chr13:52912087-52912616	HepG2	liver:	n/a	n/a
6	RXRA	chr13:52912206-52912492	HepG2	liver:	n/a	n/a
7	HNF4A	chr13:52912289-52912584	HepG2	liver:	n/a	chr13:52912361-52912376
8	HNF4A	chr13:52912134-52912524	HepG2	liver:	n/a	chr13:52912361-52912376
9	HNF4G	chr13:52912230-52912464	HepG2	liver:	n/a	chr13:52912360-52912375
10	FOXA1	chr13:52912086-52912687	HepG2	liver:	n/a	n/a
11	FOXA1	chr13:52912143-52912576	HepG2	liver:	n/a	n/a
12	SP1	chr13:52912140-52912557	HepG2	liver:	n/a	n/a
13	ARID3A	chr13:52912177-52912608	HepG2	liver:	n/a	n/a
14	E2F4	chr13:52912331-52912596	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr13:52912260-52912410	MCF-7	breast:	n/a	n/a
16	FOXA2	chr13:52911950-52912911	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52912142..52914038-chr13:53027111..53030016,2	K562	blood:
2	chr13:52911600..52913908-chr13:53027001..53029186,3	MCF-7	breast:

Variant related genes	Relation type
TPTE2P2	TF binding region
ENSG00000136108	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1056335	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap]
rs11148252	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs11618716	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs11620062	0.81[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap]
rs1327323	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs1815348	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs3803264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3886077	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3892337	0.84[CHB][hapmap]
rs4286007	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs4545703	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs4884320	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs4884354	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap]
rs4884452	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4885953	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4886018	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs4886077	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap]
rs61958050	0.80[ASN][1000 genomes]
rs6561665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7321964	0.84[CHB][hapmap]
rs7323666	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7333451	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7336679	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap]
rs7981050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7981732	0.94[ASN][1000 genomes]
rs7983971	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap]
rs7985262	0.80[ASN][1000 genomes]
rs7987115	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7990581	0.84[CHB][hapmap]
rs7993748	0.89[CHB][hapmap]
rs8001624	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap]
rs9379	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs9526913	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9526914	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535895	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9535914	0.92[CEU][hapmap]
rs9536046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9536048	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9536052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9536066	0.84[CHB][hapmap]
rs9536079	0.84[CHB][hapmap]
rs9568728	0.80[ASN][1000 genomes]
rs9568732	0.84[CHB][hapmap]
rs9596648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9596651	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv819887	chr13:52772113-52926921	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9596643	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9596643	CKAP2	cis	Thyroid	GTEx
rs9596643	CKAP2	cis	Adipose Subcutaneous	GTEx
rs9596643	CKAP2	cis	Artery Tibial	GTEx
rs9596643	CKAP2	cis	Nerve Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52911800-52913400	Enhancers	HepG2	liver
2	chr13:52912000-52912400	Enhancers	HMEC	breast
3	chr13:52912000-52913000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:52912200-52913000	Enhancers	HSMM	muscle
5	chr13:52912200-52913400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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