Variant report

Variant	rs7739563
Chromosome Location	chr6:86156315-86156316
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	POLR2A	chr6:86156238-86156381	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:86154828-86156463	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86156006..86158396-chr6:86159870..86162328,2	K562	blood:

Variant related genes	Relation type
NT5E	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1590281	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2065114	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2181187	0.82[EUR][1000 genomes]
rs2208725	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2229523	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4235826	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4235827	0.82[EUR][1000 genomes]
rs4282381	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4501401	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4562107	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707207	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6454467	0.83[EUR][1000 genomes]
rs6454468	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454469	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6931295	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7746065	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7765636	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7770359	0.81[EUR][1000 genomes]
rs9444349	0.82[EUR][1000 genomes]
rs9450272	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7739563	SNHG5	cis	Adipose Subcutaneous	GTEx
rs7739563	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs7739563	SNHG5	cis	lung	GTEx
rs7739563	SNHG5	cis	Artery Tibial	GTEx
rs7739563	SNHG5	cis	Thyroid	GTEx
rs7739563	SNHG5	cis	Muscle Skeletal	GTEx
rs7739563	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs7739563	SNHG5	cis	Whole Blood	GTEx
rs7739563	NT5E	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86129800-86157400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:86145400-86159200	Weak transcription	Gastric	stomach
3	chr6:86147200-86157800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:86152400-86158600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:86152600-86157400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:86153600-86157400	Weak transcription	HSMM	muscle
7	chr6:86154400-86157800	Weak transcription	NH-A	brain
8	chr6:86154600-86157400	Weak transcription	NHEK	skin
9	chr6:86155200-86157000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:86155200-86157400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:86155400-86156600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:86155400-86157400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:86155600-86158000	Weak transcription	HepG2	liver
14	chr6:86155800-86157400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:86155800-86157400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:86155800-86157400	Genic enhancers	NHDF-Ad	bronchial
17	chr6:86155800-86157400	Weak transcription	NHLF	lung
18	chr6:86156200-86157400	Weak transcription	Osteobl	bone

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