Variant report

Variant	rs6454469
Chromosome Location	chr6:86186475-86186476
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	chr6:86064836..86065431-chr6:86186448..86186988,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12199873	0.83[ASN][1000 genomes]
rs1590281	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2065114	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2208725	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2229523	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758840	0.81[ASN][1000 genomes]
rs2842608	0.84[ASN][1000 genomes]
rs2842609	0.84[ASN][1000 genomes]
rs2842612	0.81[ASN][1000 genomes]
rs2842613	0.81[ASN][1000 genomes]
rs4235826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4235827	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4282381	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4304137	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4373337	0.83[EUR][1000 genomes]
rs4419647	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4441928	0.88[ASN][1000 genomes]
rs4501401	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4593336	0.85[EUR][1000 genomes]
rs4706240	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4707207	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4707209	0.86[ASN][1000 genomes]
rs6454468	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6454471	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6922	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6926049	0.85[ASN][1000 genomes]
rs6931295	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7452605	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7739563	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7746065	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7761762	0.82[ASN][1000 genomes]
rs7765636	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7768065	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7770359	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9294337	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9344532	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9353318	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9362230	0.81[ASN][1000 genomes]
rs9444349	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450272	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9450282	0.82[EUR][1000 genomes]
rs9450284	0.82[ASN][1000 genomes]
rs9450287	0.82[EUR][1000 genomes]
rs9450290	0.86[AMR][1000 genomes];0.89[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6454469	SNHG5	cis	Artery Tibial	GTEx
rs6454469	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs6454469	SNHG5	cis	Heart Left Ventricle	GTEx
rs6454469	SNHG5	cis	Muscle Skeletal	GTEx
rs6454469	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs6454469	SNHG5	cis	Thyroid	GTEx
rs6454469	SNHG5	cis	multi-tissue	Pritchard
rs6454469	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs6454469	SNHG5	cis	Whole Blood	GTEx
rs6454469	SNHG5	cis	Nerve Tibial	GTEx
rs6454469	SNHG5	cis	Esophagus Mucosa	GTEx
rs6454469	SNHG5	cis	Adipose Subcutaneous	GTEx
rs6454469	SNHG5	cis	lung	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86171800-86187600	Weak transcription	Colonic Mucosa	Colon
2	chr6:86172400-86192800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:86175600-86191800	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:86176200-86187000	Strong transcription	Liver	Liver
5	chr6:86176200-86192400	Weak transcription	A549	lung
6	chr6:86176200-86192600	Weak transcription	HepG2	liver
7	chr6:86176600-86191400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:86176800-86242600	Weak transcription	Gastric	stomach
9	chr6:86178800-86206800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:86180000-86191600	Strong transcription	HSMM	muscle
11	chr6:86181000-86186800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:86182000-86192200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:86183200-86190400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:86183200-86190600	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr6:86183200-86192200	Weak transcription	HUVEC	blood vessel
16	chr6:86183600-86188200	Strong transcription	NH-A	brain
17	chr6:86183800-86188600	Strong transcription	NHDF-Ad	bronchial
18	chr6:86183800-86190200	Weak transcription	HSMMtube	muscle
19	chr6:86183800-86190600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:86183800-86191600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:86183800-86192600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:86184000-86189600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:86184200-86190200	Strong transcription	HMEC	breast
24	chr6:86184200-86191000	Strong transcription	Osteobl	bone
25	chr6:86184200-86192200	Weak transcription	Hela-S3	cervix
26	chr6:86184600-86190200	Strong transcription	NHLF	lung
27	chr6:86184800-86187200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:86185200-86186600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr6:86185200-86186800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr6:86185200-86192400	Strong transcription	NHEK	skin
31	chr6:86185200-86192600	Weak transcription	Primary T cells from cord blood	blood
32	chr6:86185400-86195600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:86185600-86187400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:86185800-86186600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:86185800-86186600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:86185800-86186800	Enhancers	Placenta	Placenta
37	chr6:86185800-86187000	ZNF genes & repeats	Ovary	ovary
38	chr6:86186000-86186600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:86186000-86186600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:86186000-86186800	ZNF genes & repeats	Aorta	Aorta
41	chr6:86186000-86186800	ZNF genes & repeats	Fetal Stomach	stomach
42	chr6:86186000-86186800	ZNF genes & repeats	Lung	lung
43	chr6:86186000-86187000	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr6:86186000-86187000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
45	chr6:86186000-86187800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:86186200-86186600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland

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