Variant report

Variant	rs1320011
Chromosome Location	chr3:156617782-156617783
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156533681..156536272-chr3:156616712..156620558,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240875	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10212230	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10936040	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs10936043	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs11712111	0.80[ASN][1000 genomes]
rs11914959	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12629380	0.82[ASN][1000 genomes]
rs12634915	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs12638253	0.94[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs13070271	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13088978	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs1319418	0.89[CEU][hapmap];1.00[TSI][hapmap]
rs1384538	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs1574980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17382070	0.82[ASN][1000 genomes]
rs1995425	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2054880	0.83[JPT][hapmap]
rs2321290	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs2321291	0.94[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2321292	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2321293	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2321455	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2874488	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2874494	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2874495	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs343994	0.83[JPT][hapmap]
rs344073	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs344080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs344082	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs344084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs344087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs416600	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4234316	0.94[CEU][hapmap]
rs4315647	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs4458324	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs453219	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680312	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4680313	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4680314	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680317	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs6441101	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6762708	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6765353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6780427	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs6780475	0.88[EUR][1000 genomes]
rs6783162	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784421	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs6803064	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7615304	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs7622309	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637701	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7638330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638625	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs873337	0.94[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs9812895	0.81[ASN][1000 genomes]
rs9814813	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs9826073	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9837038	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9844054	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9847187	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs9862338	0.90[EUR][1000 genomes]
rs9863643	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9865905	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9866373	0.84[ASN][1000 genomes]
rs9867621	0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9870137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9871817	0.94[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9876010	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs9876148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs987724	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9878585	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs9882009	0.88[EUR][1000 genomes]
rs9883439	0.94[CEU][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829765	chr3:156568263-156718496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3405756	chr3:156616308-156618631	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3355393	chr3:156616758-156618006	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1320011	LINC00886	cis	Adipose Subcutaneous	GTEx
rs1320011	LEKR1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156611600-156621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:156612000-156621200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:156616200-156617800	Enhancers	HSMMtube	muscle
4	chr3:156616600-156618400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:156616600-156621000	Weak transcription	Osteobl	bone
6	chr3:156616800-156617800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:156617000-156620200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:156617600-156617800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:156617600-156618000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:156617600-156618200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:156617600-156618400	Enhancers	HSMM	muscle

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