Variant report

Variant	rs11116969
Chromosome Location	chr12:86075981-86075982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10083104	0.83[EUR][1000 genomes]
rs10466964	0.82[EUR][1000 genomes]
rs10506924	0.84[ASN][1000 genomes]
rs10746347	0.88[ASN][1000 genomes]
rs10779164	0.82[ASN][1000 genomes]
rs10779167	0.87[ASN][1000 genomes]
rs10779168	0.87[ASN][1000 genomes]
rs10779169	0.86[ASN][1000 genomes]
rs10779170	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10779173	0.88[ASN][1000 genomes]
rs10779180	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10779181	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10779182	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10779188	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10862990	0.83[ASN][1000 genomes]
rs10862991	0.83[ASN][1000 genomes]
rs10862993	0.83[ASN][1000 genomes]
rs10862997	0.91[CHB][hapmap]
rs10862999	0.87[ASN][1000 genomes]
rs10863000	0.86[ASN][1000 genomes]
rs10863007	0.88[ASN][1000 genomes]
rs10863008	0.88[ASN][1000 genomes]
rs10863022	0.81[EUR][1000 genomes]
rs10863031	0.83[EUR][1000 genomes]
rs10863032	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863034	0.91[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs10863035	0.95[CHB][hapmap]
rs10863056	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10863057	0.84[ASN][1000 genomes]
rs11116930	0.90[ASN][1000 genomes]
rs11116934	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11116935	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11116945	0.83[EUR][1000 genomes]
rs11116964	0.81[EUR][1000 genomes]
rs11116965	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11116966	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116968	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831266	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11835161	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12308693	0.83[EUR][1000 genomes]
rs12308694	0.84[EUR][1000 genomes]
rs12578708	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17013043	0.81[EUR][1000 genomes]
rs1870933	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1870935	0.88[ASN][1000 genomes]
rs2199506	0.84[EUR][1000 genomes]
rs2199508	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2199511	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2199512	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2199513	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2199516	0.88[ASN][1000 genomes]
rs2199517	0.88[ASN][1000 genomes]
rs2199518	0.88[ASN][1000 genomes]
rs2219711	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2219718	0.84[ASN][1000 genomes]
rs2405248	0.87[ASN][1000 genomes]
rs2405254	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405256	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2405257	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2405260	0.84[EUR][1000 genomes]
rs28637596	0.81[EUR][1000 genomes]
rs2897092	0.82[EUR][1000 genomes]
rs2897094	0.84[ASN][1000 genomes]
rs34750736	0.84[EUR][1000 genomes]
rs34929726	0.82[ASN][1000 genomes]
rs4897817	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897822	0.84[ASN][1000 genomes]
rs4897825	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897837	0.84[ASN][1000 genomes]
rs4897838	0.84[ASN][1000 genomes]
rs4897842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897843	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419421	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6539899	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6539901	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539902	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7133064	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7133855	0.83[ASN][1000 genomes]
rs7134486	0.87[ASN][1000 genomes]
rs7136236	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7295445	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7297262	0.83[ASN][1000 genomes]
rs7300800	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7300819	0.83[EUR][1000 genomes]
rs7302561	0.84[ASN][1000 genomes]
rs7302629	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7303316	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7304475	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7308482	0.80[EUR][1000 genomes]
rs7310496	0.81[EUR][1000 genomes]
rs7316167	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7485084	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7485590	0.87[ASN][1000 genomes]
rs7486767	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7955601	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7959638	0.84[ASN][1000 genomes]
rs7966898	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7973153	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7973323	0.87[ASN][1000 genomes]
rs7977259	0.87[ASN][1000 genomes]
rs898986	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788015	0.88[ASN][1000 genomes]
rs9788074	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2751125	chr12:85884858-86098240	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1043253	chr12:85888151-86125364	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1052187	chr12:85954455-86278200	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv541560	chr12:85954455-86278200	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1054475	chr12:85985510-86175711	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv541561	chr12:85985510-86175711	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1042467	chr12:86017619-86078149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv983473	chr12:86055107-86079111	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
11	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11116969	RASSF9	cis	Esophagus Mucosa	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86075600-86077200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:86075800-86081600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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