Variant report

Variant	rs12212480
Chromosome Location	chr6:86458777-86458778
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86385780..86390752-chr6:86454284..86460508,14	MCF-7	breast:
2	chr6:86457332..86459007-chr6:86460736..86462827,2	MCF-7	breast:
3	chr6:86383135..86386189-chr6:86457468..86460297,4	MCF-7	breast:
4	chr6:86351009..86353966-chr6:86455070..86459127,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135316	Chromatin interaction
ENSG00000222686	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1059306	0.81[CEU][hapmap]
rs10806337	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10944136	0.97[EUR][1000 genomes]
rs10944137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10944138	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10944144	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10944145	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10944147	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10944151	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10944152	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11754330	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11755642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11758508	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12153887	0.81[EUR][1000 genomes]
rs12190603	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12191212	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12192546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12193904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196377	0.81[ASN][1000 genomes]
rs12198557	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12198730	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12199329	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12199873	0.81[CEU][hapmap]
rs12205492	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12211216	0.80[EUR][1000 genomes]
rs12212151	0.87[EUR][1000 genomes]
rs12665464	1.00[CEU][hapmap]
rs12665516	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12665542	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13201730	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13203309	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13203560	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13207173	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs13219504	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1335442	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];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1447160	0.80[EUR][1000 genomes]
rs1470531	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1813001	0.81[EUR][1000 genomes]
rs1995688	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs2084296	0.81[EUR][1000 genomes]
rs2100109	0.81[EUR][1000 genomes]
rs2121594	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs2166665	0.81[EUR][1000 genomes]
rs2197648	0.81[EUR][1000 genomes]
rs2218594	0.81[EUR][1000 genomes]
rs2225754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2324817	0.99[EUR][1000 genomes]
rs2475790	0.81[CEU][hapmap]
rs2758840	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2758846	0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2758847	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2783171	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2842601	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs2842604	1.00[ASW][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2842607	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2842608	0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2842609	0.81[CEU][hapmap]
rs2842612	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs2842613	1.00[ASW][hapmap];0.81[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs34622605	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34765423	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34795473	0.99[EUR][1000 genomes]
rs3812133	1.00[ASW][hapmap];0.80[CHD][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs4098044	0.99[EUR][1000 genomes]
rs4707223	0.89[EUR][1000 genomes]
rs4707229	0.81[EUR][1000 genomes]
rs6454487	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs6454488	0.99[EUR][1000 genomes]
rs66807489	0.96[EUR][1000 genomes]
rs67024565	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6900436	0.91[EUR][1000 genomes]
rs6928448	1.00[ASW][hapmap]
rs72907388	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7739241	1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap]
rs7742201	0.85[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs9351065	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs9362230	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs9647601	1.00[CEU][hapmap];0.99[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	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12212480	SNHG5	cis	Whole Blood	GTEx
rs12212480	SNHG5	cis	Artery Tibial	GTEx
rs12212480	SNHG5	cis	Heart Left Ventricle	GTEx
rs12212480	C6orf160	cis	lesional skin	skin_eQTL
rs12212480	SNHG5	cis	Esophagus Muscularis	GTEx
rs12212480	SNHG5	cis	Nerve Tibial	GTEx
rs12212480	SNHG5	cis	multi-tissue	Pritchard
rs12212480	SNHG5	cis	Thyroid	GTEx
rs12212480	SNHG5	cis	Adipose Subcutaneous	GTEx
rs12212480	SNHG5	cis	Muscle Skeletal	GTEx
rs12212480	C6orf160	cis	uninvolved skin	skin_eQTL
rs12212480	SNHG5	cis	Esophagus Mucosa	GTEx
rs12212480	SNHG5	cis	lung	GTEx
rs12212480	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs12212480	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86455600-86458800	Weak transcription	Fetal Intestine Large	intestine
2	chr6:86455600-86460800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:86457800-86459800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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