Variant report

Variant	rs1545200
Chromosome Location	chr4:47905817-47905818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:47902868..47906438-chr4:47914868..47916859,4	K562	blood:
2	chr4:47902691..47906376-chr4:47913835..47916673,3	K562	blood:
3	chr4:47901821..47910002-chr4:47912490..47917520,12	MCF-7	breast:
4	chr4:47899059..47902467-chr4:47904665..47908829,3	K562	blood:
5	chr4:47903871..47906617-chr4:47910701..47913086,2	K562	blood:
6	chr4:47905358..47911126-chr4:47914297..47917984,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163293	Chromatin interaction
ENSG00000170448	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10002498	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036681	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461075	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805158	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10938498	0.83[EUR][1000 genomes]
rs10938508	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11732840	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946535	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506026	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647189	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13143926	0.87[ASN][1000 genomes]
rs1371728	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1440222	1.00[ASN][1000 genomes]
rs1550444	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808853	0.84[EUR][1000 genomes]
rs1812964	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188900	1.00[ASN][1000 genomes]
rs1968542	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972883	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972884	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014934	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033894	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2033895	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119205	0.82[EUR][1000 genomes]
rs2119207	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119208	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224801	0.87[ASN][1000 genomes]
rs2352456	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352457	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352463	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352466	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581496	1.00[ASN][1000 genomes]
rs28464733	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882950	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113877	1.00[ASN][1000 genomes]
rs3113879	1.00[ASN][1000 genomes]
rs3113880	0.87[ASN][1000 genomes]
rs321625	1.00[ASN][1000 genomes]
rs321639	0.89[ASN][1000 genomes]
rs321640	1.00[ASN][1000 genomes]
rs321641	0.87[ASN][1000 genomes]
rs321647	0.87[ASN][1000 genomes]
rs321649	0.87[ASN][1000 genomes]
rs3762858	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762859	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811761	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845160	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308343	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365692	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507330	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4555602	0.82[AFR][1000 genomes]
rs4694868	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694871	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694875	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4694878	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695287	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695294	0.92[EUR][1000 genomes]
rs4695296	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4695302	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695309	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695312	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695316	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6447596	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447599	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447602	0.81[EUR][1000 genomes]
rs6815975	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819506	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826190	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832334	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833320	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845451	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850142	0.83[EUR][1000 genomes]
rs707723	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668778	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670219	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672090	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690406	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690522	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893861	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893863	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893864	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920463	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291318	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291319	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995022	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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
rs1545200	CNGA1	cis	Muscle Skeletal	GTEx
rs1545200	CNGA1	cis	Heart Left Ventricle	GTEx
rs1545200	CNGA1	cis	Thyroid	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	chr4:47876000-47906200	Weak transcription	Spleen	Spleen
8	chr4:47876000-47908600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:47876000-47915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:47876200-47915200	Weak transcription	Right Ventricle	heart
11	chr4:47876400-47915200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:47876800-47915800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:47877400-47906000	Weak transcription	Esophagus	oesophagus
14	chr4:47877400-47913800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:47877600-47913600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:47877800-47910200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:47882200-47915200	Weak transcription	Stomach Mucosa	stomach
18	chr4:47882800-47913000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:47883200-47913600	Strong transcription	HMEC	breast
20	chr4:47883200-47913800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:47883200-47914400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:47884200-47913000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:47889800-47913400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:47890000-47908000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr4:47890400-47906800	Strong transcription	GM12878-XiMat	blood
26	chr4:47890400-47913800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:47890400-47914200	Strong transcription	Liver	Liver
28	chr4:47890600-47909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:47890600-47910200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:47890800-47909600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:47890800-47913000	Strong transcription	Placenta	Placenta
32	chr4:47891400-47907800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:47892400-47907000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr4:47894600-47915200	Weak transcription	Aorta	Aorta
35	chr4:47894600-47915200	Weak transcription	Gastric	stomach
36	chr4:47895000-47913800	Weak transcription	Fetal Heart	heart
37	chr4:47895600-47907800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr4:47896400-47912600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:47896600-47906600	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr4:47897800-47909800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr4:47898200-47909200	Weak transcription	Ovary	ovary
42	chr4:47898200-47915200	Weak transcription	Small Intestine	intestine
43	chr4:47898400-47915000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:47898400-47915200	Weak transcription	Colonic Mucosa	Colon
45	chr4:47898600-47915200	Weak transcription	Fetal Brain Male	brain
46	chr4:47899600-47915600	Weak transcription	Lung	lung
47	chr4:47899800-47906200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:47899800-47915000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr4:47899800-47915200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:47899800-47915200	Weak transcription	Brain Substantia Nigra	brain

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