Variant report

Variant	rs7641452
Chromosome Location	chr3:42941115-42941116
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42844539..42847348-chr3:42939373..42941976,2	MCF-7	breast:
2	chr3:42936127..42937782-chr3:42940399..42942185,2	K562	blood:
3	chr3:42935964..42938886-chr3:42940569..42942633,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KRBOX1-1	chr3:42938530-42941828	ENSG00000273328.1

Variant related genes	Relation type
ENSG00000181061	Chromatin interaction
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10470680	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129987	0.81[EUR][1000 genomes]
rs11129988	0.81[EUR][1000 genomes]
rs123506	1.00[CHB][hapmap]
rs12629332	1.00[CHB][hapmap]
rs1346414	0.81[EUR][1000 genomes]
rs1346415	0.81[EUR][1000 genomes]
rs1392319	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1403525	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17074894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238972	1.00[ASN][1000 genomes]
rs1816227	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28378297	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601753	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655956	1.00[ASN][1000 genomes]
rs28673478	1.00[ASN][1000 genomes]
rs339661	1.00[CHB][hapmap]
rs339682	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs339683	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs339686	1.00[CHB][hapmap]
rs3915020	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4404423	1.00[CHB][hapmap]
rs489117	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs530842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs534284	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs542394	0.80[EUR][1000 genomes]
rs545023	0.80[EUR][1000 genomes]
rs551658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604393	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs60616619	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61004728	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617014	1.00[ASN][1000 genomes]
rs62248962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249006	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249007	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249008	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249009	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249011	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249013	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249014	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249015	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62249016	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249584	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs651899	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6763762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773223	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775999	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782601	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs678310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6798412	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798520	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs680967	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs681341	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs73075297	1.00[ASN][1000 genomes]
rs73075301	1.00[ASN][1000 genomes]
rs73077208	1.00[ASN][1000 genomes]
rs73077214	1.00[ASN][1000 genomes]
rs73077238	1.00[ASN][1000 genomes]
rs73087348	1.00[ASN][1000 genomes]
rs735320	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs73832423	1.00[ASN][1000 genomes]
rs73832424	1.00[ASN][1000 genomes]
rs7617715	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625959	0.94[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs7644923	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834579	1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs834584	1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap]
rs9311330	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808932	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815609	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9816391	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9824700	1.00[ASN][1000 genomes]
rs9828785	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs9832875	1.00[ASW][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9833284	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837761	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840349	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9852930	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858270	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862469	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9865715	1.00[CHB][hapmap]
rs9870478	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3783	chr3:42926223-42970597	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7641452	HIGD1A	cis	cerebellum	SCAN
rs7641452	KIF15	cis	parietal	SCAN
rs7641452	HHATL	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42933800-42941800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:42939600-42944000	Enhancers	Placenta	Placenta
3	chr3:42940000-42944000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr3:42940000-42944400	Enhancers	Stomach Mucosa	stomach
5	chr3:42940200-42941600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:42940800-42941200	Weak transcription	NHEK	skin

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