Variant report

Variant	rs13214489
Chromosome Location	chr6:86568782-86568783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10944157	0.92[AMR][1000 genomes]
rs11752180	0.98[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11752223	0.97[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12153887	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12198061	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12202712	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12209668	0.98[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12211216	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12660846	0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12665464	0.98[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13207537	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13209671	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13209740	0.92[AMR][1000 genomes]
rs13213603	0.81[AMR][1000 genomes]
rs1447160	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1813001	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1838954	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1838955	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1838958	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1838959	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2084293	0.97[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2084294	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2084296	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2084297	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2100109	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2166665	0.84[AMR][1000 genomes]
rs2197648	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2218594	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35874630	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs36035797	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4706246	0.84[AMR][1000 genomes]
rs4706248	0.81[AMR][1000 genomes]
rs4706252	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4706253	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4707229	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57016132	0.92[AMR][1000 genomes]
rs7739241	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7755730	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv515896	chr6:86538718-86573165	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh	lncRNA	n/a	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13214489	SNHG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 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	chr6:86566600-86573400	Weak transcription	Pancreas	Pancrea
3	chr6:86566800-86574200	Weak transcription	Ovary	ovary
4	chr6:86568200-86576800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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