Variant report

Variant	rs12660846
Chromosome Location	chr6:86573809-86573810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86386983..86389313-chr6:86573645..86576019,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10944136	0.83[ASN][1000 genomes]
rs10944144	0.91[EUR][1000 genomes]
rs10944145	0.91[EUR][1000 genomes]
rs10944147	0.92[EUR][1000 genomes]
rs10944151	0.91[EUR][1000 genomes]
rs10944152	0.91[EUR][1000 genomes]
rs10944157	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11752180	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11752223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11758508	0.82[EUR][1000 genomes]
rs12153887	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12190603	0.83[ASN][1000 genomes]
rs12191212	0.91[EUR][1000 genomes]
rs12196377	0.95[EUR][1000 genomes]
rs12198061	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12198557	0.86[EUR][1000 genomes]
rs12198730	0.92[EUR][1000 genomes]
rs12199329	0.91[EUR][1000 genomes]
rs12201741	0.81[EUR][1000 genomes]
rs12202712	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12209668	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12211216	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12215159	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12216103	0.81[ASN][1000 genomes]
rs12664634	0.81[ASN][1000 genomes]
rs12665464	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665516	0.91[EUR][1000 genomes]
rs12665542	0.91[EUR][1000 genomes]
rs13192974	0.82[ASN][1000 genomes]
rs13199006	0.82[ASN][1000 genomes]
rs13201730	0.92[EUR][1000 genomes]
rs13203309	0.91[EUR][1000 genomes]
rs13203560	0.92[EUR][1000 genomes]
rs13207173	0.82[ASN][1000 genomes]
rs13207537	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13209671	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13209740	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213603	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13214489	0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13219504	0.92[EUR][1000 genomes]
rs1447160	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1470531	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1813001	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1838954	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1838955	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1838956	0.80[ASN][1000 genomes]
rs1838957	0.81[ASN][1000 genomes]
rs1838958	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1838959	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2084293	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2084294	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2084296	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2084297	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2100109	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2121594	0.97[EUR][1000 genomes]
rs2166665	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2197648	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2218594	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2324817	0.82[ASN][1000 genomes]
rs2875456	0.81[EUR][1000 genomes]
rs34795473	0.82[ASN][1000 genomes]
rs35874630	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36035797	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36053156	0.99[EUR][1000 genomes]
rs4098044	0.82[ASN][1000 genomes]
rs4706246	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4706247	0.81[AMR][1000 genomes]
rs4706248	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4706252	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4706253	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4706254	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707223	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4707229	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707236	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4707239	0.82[ASN][1000 genomes]
rs57016132	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61119084	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6454487	0.81[ASN][1000 genomes]
rs6454488	0.82[ASN][1000 genomes]
rs6454504	0.81[ASN][1000 genomes]
rs66807489	0.81[ASN][1000 genomes]
rs67024565	0.92[EUR][1000 genomes]
rs6900436	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7739241	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7755730	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7766645	0.82[ASN][1000 genomes]
rs9647601	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028293	chr6:86353958-86778912	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
2	nsv538350	chr6:86353958-86778912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
3	nsv886335	chr6:86445651-86669361	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1022618	chr6:86465365-87432069	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538352	chr6:86465365-87432069	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1033637	chr6:86482045-86701733	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538353	chr6:86482045-86701733	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv526067	chr6:86538718-86576854	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1802672	chr6:86546123-86662267	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv522858	chr6:86550985-86578833	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1018453	chr6:86555984-86761120	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3451810	chr6:86564474-86577360	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12660846	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs12660846	SNHG5	cis	Esophagus Muscularis	GTEx
rs12660846	SNHG5	cis	Esophagus Mucosa	GTEx
rs12660846	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs12660846	SNHG5	cis	Whole Blood	GTEx
rs12660846	SNHG5	cis	multi-tissue	Pritchard
rs12660846	SNHG5	cis	Muscle Skeletal	GTEx
rs12660846	SNHG5	cis	Heart Left Ventricle	GTEx
rs12660846	SNHG5	cis	Adipose Subcutaneous	GTEx
rs12660846	SNHG5	cis	Artery Tibial	GTEx
rs12660846	SNHG5	cis	lung	GTEx
rs12660846	SNHG5	cis	Nerve Tibial	GTEx
rs12660846	SNHG5	cis	Artery Aorta	GTEx
rs12660846	SNHG5	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86563200-86577800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:86566800-86574200	Weak transcription	Ovary	ovary
3	chr6:86568200-86576800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:86572400-86574800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:86573400-86575600	Enhancers	Pancreas	Pancrea
6	chr6:86573600-86574400	Weak transcription	Esophagus	oesophagus
7	chr6:86573800-86574800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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