Variant report

Variant	rs1173417
Chromosome Location	chr6:86403941-86403942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86385642..86390131-chr6:86401946..86405248,5	K562	blood:

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 20 )

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

rs_ID	r²[population]
rs1059306	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs1059307	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs10806334	0.83[EUR][1000 genomes]
rs10944133	0.80[EUR][1000 genomes]
rs1173418	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs12190603	0.90[CHB][hapmap]
rs12199873	0.83[CEU][hapmap]
rs12203963	0.83[CEU][hapmap]
rs12212560	0.87[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13207173	0.86[CHB][hapmap]
rs1470531	0.82[CHB][hapmap]
rs2475787	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2475790	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2475791	0.81[EUR][1000 genomes]
rs2475792	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]
rs2484355	0.81[EUR][1000 genomes]
rs2758840	0.83[CEU][hapmap]
rs2758842	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2758843	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2758845	0.91[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2758847	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2758848	0.83[CEU][hapmap]
rs2783171	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2842600	0.83[CEU][hapmap]
rs2842601	0.83[CEU][hapmap]
rs2842603	0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2842604	0.82[EUR][1000 genomes]
rs2842607	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2842608	0.83[CEU][hapmap]
rs2842609	0.83[CEU][hapmap]
rs2842611	0.83[CEU][hapmap]
rs2842612	0.82[CEU][hapmap]
rs2842613	0.83[CEU][hapmap]
rs2842614	0.91[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2842617	0.88[EUR][1000 genomes]
rs3087978	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs3812133	0.82[EUR][1000 genomes]
rs4304137	0.83[CEU][hapmap]
rs4348284	0.83[CEU][hapmap]
rs4351223	0.83[CEU][hapmap]
rs4383777	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707211	0.83[CEU][hapmap]
rs6454471	0.83[CEU][hapmap]
rs6454486	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454487	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs6909767	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs6922	0.83[CEU][hapmap]
rs6935918	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs7452605	0.83[CEU][hapmap]
rs7739241	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs7742201	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7742691	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs7752502	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757864	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7762321	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7771612	0.83[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7775864	0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs911927	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9294337	0.83[CEU][hapmap]
rs9342041	0.87[EUR][1000 genomes]
rs9342044	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9342046	0.88[ASN][1000 genomes]
rs9344533	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9344542	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[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]
rs9351065	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs9353318	0.83[CEU][hapmap]
rs9353320	0.87[EUR][1000 genomes]
rs9353327	0.92[ASW][hapmap];0.87[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]
rs9359658	0.85[EUR][1000 genomes]
rs9362230	0.83[CEU][hapmap]
rs9362233	0.80[EUR][1000 genomes]
rs9362239	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444352	0.83[CEU][hapmap]
rs9450285	0.83[CEU][hapmap]
rs9450302	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs9450318	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450319	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9647601	0.86[CHB][hapmap]

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	nsv970049	chr6:86395496-86410652	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs1173417	SNHG5	cis	Heart Left Ventricle	GTEx
rs1173417	C6orf160	cis	normal skin	skin_eQTL
rs1173417	SNHG5	cis	lung	GTEx
rs1173417	SNHG5	cis	Artery Tibial	GTEx
rs1173417	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs1173417	SNHG5	cis	Esophagus Mucosa	GTEx
rs1173417	SNHG5	cis	Stomach	GTEx
rs1173417	SNHG5	cis	Artery Aorta	GTEx
rs1173417	SNHG5	cis	Thyroid	GTEx
rs1173417	SNHG5	cis	Muscle Skeletal	GTEx
rs1173417	C6orf160	cis	uninvolved skin	skin_eQTL
rs1173417	SNHG5	cis	Esophagus Muscularis	GTEx
rs1173417	SNHG5	cis	lymphoblastoid	seeQTL
rs1173417	SNHG5	cis	multi-tissue	Pritchard
rs1173417	C6orf160	cis	lesional skin	skin_eQTL
rs1173417	SNHG5	cis	Whole Blood	GTEx
rs1173417	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs1173417	SNHG5	cis	Nerve Tibial	GTEx
rs1173417	NT5E	cis	lymphoblastoid	seeQTL
rs1173417	SNHG5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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