Variant report

Variant	rs6447592
Chromosome Location	chr4:47898491-47898492
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	chr4:47887965..47889707-chr4:47897054..47899233,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10025104	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10030927	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938503	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503789	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1371730	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1440227	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1507922	0.89[EUR][1000 genomes]
rs1583808	0.89[ASN][1000 genomes]
rs16860723	0.93[ASN][1000 genomes]
rs2033897	0.90[ASN][1000 genomes]
rs2033898	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053404	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289433	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2352145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529019	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4694867	0.90[ASN][1000 genomes]
rs4694872	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4695277	0.90[ASN][1000 genomes]
rs4695285	0.90[ASN][1000 genomes]
rs4695286	0.90[ASN][1000 genomes]
rs4695290	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695292	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695300	0.93[ASN][1000 genomes]
rs4695303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695306	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695307	0.92[ASN][1000 genomes]
rs4695308	0.92[ASN][1000 genomes]
rs57010305	0.93[ASN][1000 genomes]
rs58511183	0.93[ASN][1000 genomes]
rs60427744	0.93[ASN][1000 genomes]
rs60515154	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414687	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6447586	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447593	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811385	0.93[ASN][1000 genomes]
rs6816082	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818556	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822668	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6827508	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6844286	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238638	0.88[ASN][1000 genomes]
rs73238639	0.90[ASN][1000 genomes]
rs73244433	0.90[ASN][1000 genomes]
rs73244436	0.91[ASN][1000 genomes]
rs73244437	0.92[ASN][1000 genomes]
rs73244438	0.93[ASN][1000 genomes]
rs73244439	0.93[ASN][1000 genomes]
rs73244442	0.90[ASN][1000 genomes]
rs7663935	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7687363	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7690562	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920462	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9291317	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9683791	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
7	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6447592	CNGA1	cis	Muscle Skeletal	GTEx
rs6447592	CNGA1	cis	Thyroid	GTEx
rs6447592	CNGA1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47865400-47913400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:47872400-47911600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr4:47873400-47913400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:47873600-47910600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:47874400-47913400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:47874400-47913600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:47875800-47903000	Strong transcription	Dnd41	blood
8	chr4:47876000-47906200	Weak transcription	Spleen	Spleen
9	chr4:47876000-47908600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:47876000-47915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:47876200-47900800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:47876200-47915200	Weak transcription	Right Ventricle	heart
13	chr4:47876400-47915200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:47876600-47905400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:47876800-47915800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:47877400-47906000	Weak transcription	Esophagus	oesophagus
17	chr4:47877400-47913800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:47877600-47913600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:47877800-47910200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:47882200-47915200	Weak transcription	Stomach Mucosa	stomach
21	chr4:47882800-47913000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:47883000-47902200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:47883000-47902400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:47883200-47913600	Strong transcription	HMEC	breast
25	chr4:47883200-47913800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:47883200-47914400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:47883400-47904400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr4:47883800-47902600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr4:47884200-47913000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:47886200-47898600	Weak transcription	A549	lung
31	chr4:47888000-47900800	Weak transcription	Pancreas	Pancrea
32	chr4:47888800-47901800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:47888800-47902200	Weak transcription	Fetal Stomach	stomach
34	chr4:47889200-47903000	Strong transcription	HUVEC	blood vessel
35	chr4:47889400-47902200	Strong transcription	Adipose Nuclei	Adipose
36	chr4:47889800-47913400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:47890000-47908000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:47890200-47902600	Strong transcription	Osteobl	bone
39	chr4:47890400-47898600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:47890400-47906800	Strong transcription	GM12878-XiMat	blood
41	chr4:47890400-47913800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:47890400-47914200	Strong transcription	Liver	Liver
43	chr4:47890600-47901000	Strong transcription	Primary hematopoietic stem cells	blood
44	chr4:47890600-47901600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:47890600-47902000	Strong transcription	NH-A	brain
46	chr4:47890600-47902200	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr4:47890600-47902400	Strong transcription	HepG2	liver
48	chr4:47890600-47902800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:47890600-47905000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:47890600-47909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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