Variant report

Variant	rs2475792
Chromosome Location	chr6:86392102-86392103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr6:86391611-86392106	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
SNHG5	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1059306	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs1059307	0.91[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap]
rs1173417	0.92[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1173418	0.83[CHB][hapmap]
rs12190603	0.90[CHB][hapmap]
rs12199873	0.86[CEU][hapmap]
rs12203963	0.86[CEU][hapmap]
rs12212560	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13207173	0.86[CHB][hapmap]
rs1470531	0.82[CHB][hapmap]
rs1885607	0.86[EUR][1000 genomes]
rs2475787	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2475790	0.86[CEU][hapmap]
rs2484355	0.88[EUR][1000 genomes]
rs2758840	0.86[CEU][hapmap]
rs2758842	0.83[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs2758843	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2758845	0.83[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2758846	0.82[CEU][hapmap]
rs2758847	0.86[CEU][hapmap]
rs2758848	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs2783171	0.86[CEU][hapmap]
rs2842600	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs2842601	0.86[CEU][hapmap]
rs2842603	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842604	0.82[CEU][hapmap]
rs2842607	0.86[CEU][hapmap]
rs2842608	0.86[CEU][hapmap]
rs2842609	0.86[CEU][hapmap]
rs2842611	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs2842612	0.86[CEU][hapmap]
rs2842613	0.86[CEU][hapmap]
rs2842614	0.95[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs2842617	0.86[EUR][1000 genomes]
rs3087978	0.86[CEU][hapmap];0.83[CHB][hapmap]
rs3812133	0.82[CEU][hapmap]
rs4304137	0.86[CEU][hapmap]
rs4348284	0.86[CEU][hapmap]
rs4351223	0.86[CEU][hapmap]
rs4383777	0.86[ASN][1000 genomes]
rs4441928	0.82[CEU][hapmap]
rs4707211	0.86[CEU][hapmap]
rs6454471	0.86[CEU][hapmap]
rs6454472	0.82[CEU][hapmap];0.81[MEX][hapmap]
rs6454486	0.84[ASN][1000 genomes]
rs6454487	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs6909767	0.95[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6922	0.86[CEU][hapmap]
rs6935918	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs7452605	0.86[CEU][hapmap]
rs7739241	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs7742201	0.86[CEU][hapmap]
rs7742691	0.83[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap]
rs7752502	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757864	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7762321	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7766485	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs7771612	0.91[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs7775864	0.82[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs911927	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9294337	0.86[CEU][hapmap]
rs9342041	0.85[EUR][1000 genomes]
rs9342044	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9342046	0.86[ASN][1000 genomes]
rs9344532	0.82[CEU][hapmap]
rs9344533	0.95[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs9344542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9351065	0.86[CEU][hapmap]
rs9353318	0.86[CEU][hapmap]
rs9353320	0.85[EUR][1000 genomes]
rs9353327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9359658	0.83[EUR][1000 genomes]
rs9362230	0.86[CEU][hapmap]
rs9362239	0.84[ASN][1000 genomes]
rs9444352	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs9450282	0.82[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs9450285	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs9450288	0.86[MEX][hapmap]
rs9450302	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs9450318	0.86[ASN][1000 genomes]
rs9450319	0.85[ASN][1000 genomes]
rs9647601	0.86[CHB][hapmap]

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	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2475792	C6orf160	cis	uninvolved skin	skin_eQTL
rs2475792	SNHG5	cis	Muscle Skeletal	GTEx
rs2475792	SNHG5	cis	lymphoblastoid	seeQTL
rs2475792	SNHG5	cis	Esophagus Muscularis	GTEx
rs2475792	SNHG5	cis	Adipose Subcutaneous	GTEx
rs2475792	SNHG5	cis	multi-tissue	Pritchard
rs2475792	SNHG5	cis	Artery Aorta	GTEx
rs2475792	C6orf160	cis	lesional skin	skin_eQTL
rs2475792	SNHG5	cis	Heart Left Ventricle	GTEx
rs2475792	SNHG5	cis	Stomach	GTEx
rs2475792	C6orf160	cis	multi-tissue	Pritchard
rs2475792	SNHG5	cis	Thyroid	GTEx
rs2475792	SNHG5	cis	Esophagus Mucosa	GTEx
rs2475792	C6orf160	cis	normal skin	skin_eQTL
rs2475792	SNHG5	cis	lung	GTEx
rs2475792	SNHG5	cis	Nerve Tibial	GTEx
rs2475792	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs2475792	SNHG5	cis	Artery Tibial	GTEx
rs2475792	SNORD50B	cis	parietal	SCAN
rs2475792	SNHG5	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86389600-86393200	Weak transcription	Psoas Muscle	Psoas
2	chr6:86390400-86393800	Weak transcription	NHLF	lung
3	chr6:86390400-86394000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:86390400-86394200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:86390400-86395200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:86390600-86392800	Weak transcription	A549	lung
7	chr6:86390600-86392800	Enhancers	Dnd41	blood
8	chr6:86390600-86394600	Weak transcription	GM12878-XiMat	blood

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