Variant report

Variant	rs6590849
Chromosome Location	chr11:101218094-101218095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:101206973..101209603-chr11:101215324..101218804,5	MCF-7	breast:
2	chr11:101204850..101206568-chr11:101216370..101218964,2	MCF-7	breast:
3	chr11:100997445..101001365-chr11:101215076..101220609,8	MCF-7	breast:
4	chr11:101211140..101214138-chr11:101214297..101218139,4	MCF-7	breast:
5	chr11:101216604..101219529-chr11:101221127..101223365,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082175	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10458946	0.85[EUR][1000 genomes]
rs10791460	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10791461	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10895097	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10895098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895099	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11224719	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11224720	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11224722	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11224723	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11224725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11224728	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11224729	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11224748	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11224752	0.85[EUR][1000 genomes]
rs11224753	0.85[EUR][1000 genomes]
rs11224754	0.85[EUR][1000 genomes]
rs11224755	0.85[EUR][1000 genomes]
rs11224756	0.85[EUR][1000 genomes]
rs11224758	0.85[EUR][1000 genomes]
rs12223715	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12226605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12575087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12576141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12790159	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12792457	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12795880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12795968	0.85[EUR][1000 genomes]
rs12796333	0.85[EUR][1000 genomes]
rs12798288	0.85[EUR][1000 genomes]
rs12802904	0.85[EUR][1000 genomes]
rs12803560	0.85[EUR][1000 genomes]
rs12803803	0.85[EUR][1000 genomes]
rs12803811	0.85[EUR][1000 genomes]
rs12804031	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12804791	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12806219	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938972	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1938978	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938979	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938987	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1938989	0.80[EUR][1000 genomes]
rs1938991	0.85[EUR][1000 genomes]
rs1938994	0.81[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs1943766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1943767	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1943768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2155047	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2155048	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508354	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2508357	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2508358	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2508359	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2508360	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2508362	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2508365	0.87[EUR][1000 genomes]
rs2508366	0.87[EUR][1000 genomes]
rs2508367	0.87[EUR][1000 genomes]
rs2508368	0.81[EUR][1000 genomes]
rs2508369	0.87[EUR][1000 genomes]
rs2508371	0.87[EUR][1000 genomes]
rs2508372	0.86[EUR][1000 genomes]
rs2508375	0.87[EUR][1000 genomes]
rs2513146	0.88[EUR][1000 genomes]
rs2513149	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2513150	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2513151	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2513152	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2513153	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2513154	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2513168	0.87[EUR][1000 genomes]
rs2513169	0.87[EUR][1000 genomes]
rs2513170	0.87[EUR][1000 genomes]
rs2513172	0.86[EUR][1000 genomes]
rs2513174	0.87[EUR][1000 genomes]
rs2513175	0.87[EUR][1000 genomes]
rs2513176	0.87[EUR][1000 genomes]
rs2513178	0.82[EUR][1000 genomes]
rs3016236	0.81[AFR][1000 genomes]
rs3018696	0.87[EUR][1000 genomes]
rs35180268	0.86[EUR][1000 genomes]
rs35452558	0.85[EUR][1000 genomes]
rs35539851	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3949114	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4388857	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4582936	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4754010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4754750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4754754	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57177149	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58151663	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6590848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6590850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6590854	0.86[EUR][1000 genomes]
rs66975288	0.88[EUR][1000 genomes]
rs7121801	0.86[EUR][1000 genomes]
rs72980010	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72980011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs744021	0.85[EUR][1000 genomes]
rs7481005	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7924880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7924990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7925121	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7925790	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7926811	0.83[EUR][1000 genomes]
rs7928176	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7928303	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938688	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7939471	0.85[EUR][1000 genomes]
rs7940365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7940483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7948589	0.88[EUR][1000 genomes]
rs9787788	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556131	chr11:100985777-101480017	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530644	chr11:101010088-101486038	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	esv2753322	chr11:101052790-101311790	Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv832247	chr11:101123483-101298787	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv898329	chr11:101152961-101218094	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6590849	MMP27	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101215000-101218200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:101216800-101218200	Enhancers	Ovary	ovary
3	chr11:101216800-101218200	Enhancers	NHDF-Ad	bronchial

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