Variant report

Variant	rs9344542
Chromosome Location	chr6:86393905-86393906
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	chr6:86392546..86395306-chr6:86396739..86401474,7	K562	blood:
2	chr6:85472016..85474374-chr6:86392649..86394394,2	K562	blood:

Variant related genes	Relation type
ENSG00000112837	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 21 )

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

rs_ID	r²[population]
rs1059306	0.87[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];0.87[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]
rs1173418	0.83[CHB][hapmap]
rs12190603	0.90[CHB][hapmap]
rs12199873	0.87[CEU][hapmap]
rs12203963	0.87[CEU][hapmap]
rs12212560	0.91[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][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	0.87[CEU][hapmap]
rs2475792	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]
rs2484355	0.88[EUR][1000 genomes]
rs2758840	0.87[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];0.91[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];0.93[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	0.87[CEU][hapmap]
rs2758848	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs2783171	0.87[CEU][hapmap]
rs2842600	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs2842601	0.87[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	0.87[CEU][hapmap]
rs2842608	0.87[CEU][hapmap]
rs2842609	0.87[CEU][hapmap]
rs2842611	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs2842612	0.86[CEU][hapmap]
rs2842613	0.87[CEU][hapmap]
rs2842614	0.95[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.84[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	0.87[CEU][hapmap]
rs4348284	0.87[CEU][hapmap]
rs4351223	0.87[CEU][hapmap]
rs4383777	0.86[ASN][1000 genomes]
rs4441928	0.82[CEU][hapmap]
rs4707211	0.87[CEU][hapmap]
rs6454471	0.87[CEU][hapmap]
rs6454472	0.83[CEU][hapmap];0.82[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	0.87[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	0.87[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];0.86[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	0.83[CEU][hapmap];0.86[MEX][hapmap]
rs7771612	0.87[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	0.95[GIH][hapmap];0.81[JPT][hapmap];0.86[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	0.87[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]
rs9351065	0.87[CEU][hapmap]
rs9353318	0.87[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];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]
rs9359658	0.83[EUR][1000 genomes]
rs9362230	0.87[CEU][hapmap]
rs9362239	0.84[ASN][1000 genomes]
rs9444352	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs9450282	0.83[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs9450285	0.87[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:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs9344542	SNHG5	cis	Artery Aorta	GTEx
rs9344542	C6orf160	cis	uninvolved skin	skin_eQTL
rs9344542	SNORD50B	cis	parietal	SCAN
rs9344542	C6orf160	cis	normal skin	skin_eQTL
rs9344542	SNHG5	cis	Heart Left Ventricle	GTEx
rs9344542	SNHG5	cis	Esophagus Muscularis	GTEx
rs9344542	SNHG5	cis	Nerve Tibial	GTEx
rs9344542	SNHG5	cis	multi-tissue	Pritchard
rs9344542	SNHG5	cis	Whole Blood	GTEx
rs9344542	C6orf160	cis	multi-tissue	Pritchard
rs9344542	SNHG5	cis	lung	GTEx
rs9344542	SNHG5	cis	Artery Tibial	GTEx
rs9344542	SNHG5	cis	Adipose Subcutaneous	GTEx
rs9344542	SNHG5	cis	Muscle Skeletal	GTEx
rs9344542	SNHG5	cis	lymphoblastoid	seeQTL
rs9344542	SNHG5	cis	Stomach	GTEx
rs9344542	SNHG5	cis	Thyroid	GTEx
rs9344542	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs9344542	SNHG5	cis	Esophagus Mucosa	GTEx
rs9344542	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs9344542	C6orf160	cis	lesional skin	skin_eQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86390400-86394000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:86390400-86394200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr6:86390400-86395200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:86390600-86394600	Weak transcription	GM12878-XiMat	blood
5	chr6:86393600-86394600	Weak transcription	Psoas Muscle	Psoas
6	chr6:86393800-86394800	Enhancers	NHLF	lung

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