Variant report

Variant	rs13068298
Chromosome Location	chr3:143772247-143772248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143690072..143692415-chr3:143771127..143773744,2	MCF-7	breast:
2	chr3:143735422..143737968-chr3:143770929..143772909,2	K562	blood:
3	chr3:143691918..143694518-chr3:143770201..143772805,2	K562	blood:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1025984	1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.80[TSI][hapmap];0.91[ASN][1000 genomes]
rs10513235	1.00[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs11914731	0.89[ASN][1000 genomes]
rs11924473	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13067695	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078840	1.00[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs13081286	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs13086088	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs13091882	0.81[EUR][1000 genomes]
rs1466941	0.93[GIH][hapmap]
rs16854816	0.90[ASN][1000 genomes]
rs16854819	0.90[ASN][1000 genomes]
rs16854884	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16854886	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867608	0.91[ASN][1000 genomes]
rs1867609	0.91[ASN][1000 genomes]
rs1898265	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1961542	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979910	0.86[GIH][hapmap]
rs2011080	0.90[ASN][1000 genomes]
rs2164554	0.99[ASN][1000 genomes]
rs2370171	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34372603	0.90[ASN][1000 genomes]
rs34639473	0.84[EUR][1000 genomes]
rs34683397	0.97[ASN][1000 genomes]
rs34730687	0.91[EUR][1000 genomes]
rs35067746	0.90[ASN][1000 genomes]
rs35193361	0.95[ASN][1000 genomes]
rs35309714	0.90[ASN][1000 genomes]
rs35629416	0.99[ASN][1000 genomes]
rs35649888	0.89[ASN][1000 genomes]
rs35788195	0.97[ASN][1000 genomes]
rs35796781	0.99[ASN][1000 genomes]
rs35885310	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35887108	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35959290	0.99[ASN][1000 genomes]
rs4527375	0.90[ASN][1000 genomes]
rs4561830	0.90[ASN][1000 genomes]
rs4611822	0.91[ASN][1000 genomes]
rs4613453	0.90[ASN][1000 genomes]
rs4616638	0.90[ASN][1000 genomes]
rs58251824	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59768870	0.88[ASN][1000 genomes]
rs60367530	0.95[ASN][1000 genomes]
rs60676654	0.90[ASN][1000 genomes]
rs62268458	0.98[ASN][1000 genomes]
rs62269895	0.91[ASN][1000 genomes]
rs62269933	0.84[EUR][1000 genomes]
rs6440210	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs6440212	0.90[ASN][1000 genomes]
rs6766544	0.90[ASN][1000 genomes]
rs6766685	0.90[ASN][1000 genomes]
rs6767236	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769910	0.90[ASN][1000 genomes]
rs6778627	0.88[ASN][1000 genomes]
rs6779321	0.90[ASN][1000 genomes]
rs6782024	0.80[EUR][1000 genomes]
rs6783089	0.90[ASN][1000 genomes]
rs6784938	0.81[EUR][1000 genomes]
rs6786460	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6791078	0.90[ASN][1000 genomes]
rs6795008	0.88[ASN][1000 genomes]
rs6796460	0.90[ASN][1000 genomes]
rs6804060	0.84[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs7610378	0.90[GIH][hapmap];0.80[TSI][hapmap]
rs7611326	0.89[ASN][1000 genomes]
rs7634145	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs7637912	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs7639366	0.89[ASN][1000 genomes]
rs7642551	0.90[ASN][1000 genomes]
rs7642774	0.88[ASN][1000 genomes]
rs7646187	0.99[ASN][1000 genomes]
rs7649614	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7650145	0.81[ASN][1000 genomes]
rs7650172	0.89[ASN][1000 genomes]
rs7653331	0.82[EUR][1000 genomes]
rs920159	0.91[ASN][1000 genomes]
rs951865	0.81[EUR][1000 genomes]
rs9755502	0.88[ASN][1000 genomes]
rs9755515	0.87[ASN][1000 genomes]
rs989665	0.87[EUR][1000 genomes]

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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1010117	chr3:143750590-144093775	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv536748	chr3:143750590-144093775	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv877569	chr3:143762420-143825439	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Economic and political preferences (feminism/equality)	22566634	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13068298	C3orf58	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143768000-143772800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:143770400-143772400	Weak transcription	HSMMtube	muscle
3	chr3:143770600-143772400	Weak transcription	HSMM	muscle
4	chr3:143771400-143772400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:143772200-143772400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:143772200-143773000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:143772200-143773000	Enhancers	Brain Angular Gyrus	brain
8	chr3:143772200-143773000	Enhancers	Brain Substantia Nigra	brain
9	chr3:143772200-143773000	Enhancers	NH-A	brain
10	chr3:143772200-143773000	Enhancers	NHEK	skin
11	chr3:143772200-143773000	Enhancers	Osteobl	bone
12	chr3:143772200-143773200	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:143772200-143773200	Enhancers	NHDF-Ad	bronchial
14	chr3:143772200-143775600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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