Variant report

Variant	rs1405645
Chromosome Location	chr2:178853378-178853379
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178852131..178854988-chr2:178855154..178857922,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10930814	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.80[MKK][hapmap]
rs11695211	0.83[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12463866	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs12469439	0.81[CHB][hapmap];0.90[ASN][1000 genomes]
rs12615720	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1369519	0.87[ASN][1000 genomes]
rs1369520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1405643	1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs1405644	0.80[ASN][1000 genomes]
rs1405646	0.87[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs1435575	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1534290	1.00[YRI][hapmap]
rs16865995	1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs16866042	1.00[YRI][hapmap]
rs1821628	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880915	0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs2020213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2037757	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2099476	1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs2217839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2573080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2573081	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2573083	0.82[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap]
rs2573085	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2573088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2695094	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2695103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695104	0.87[ASN][1000 genomes]
rs2695111	0.80[ASN][1000 genomes]
rs2695112	0.87[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2695729	0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2695735	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs2695738	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2695743	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2695744	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2695746	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2695747	0.82[CHB][hapmap]
rs2695750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs2695752	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2695754	0.80[ASN][1000 genomes]
rs2695760	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3108453	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs3108476	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs6433705	0.81[CHB][hapmap];0.90[ASN][1000 genomes]
rs6743194	1.00[YRI][hapmap]
rs6745288	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7573622	1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs7604345	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs934807	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs959792	0.82[CHB][hapmap]
rs966433	0.83[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1007579	chr2:178729330-178890946	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875451	chr2:178748294-178953409	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv998304	chr2:178756380-178924378	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv536056	chr2:178756380-178924378	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv583712	chr2:178843950-178857169	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv521228	chr2:178845469-178856900	Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv583718	chr2:178845469-178857169	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv583731	chr2:178845755-178857169	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv583736	chr2:178851177-178857169	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1405645	SP3	cis	parietal	SCAN
rs1405645	FKBP7	cis	parietal	SCAN
rs1405645	PRKRA	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178850000-178854000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:178850000-178854200	Weak transcription	Fetal Intestine Large	intestine
3	chr2:178853000-178854600	Enhancers	A549	lung
4	chr2:178853200-178854200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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