Variant report

Variant	rs1371730
Chromosome Location	chr4:47908604-47908605
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:47901843..47903515-chr4:47906102..47908734,2	MCF-7	breast:
2	chr4:47892858..47895013-chr4:47908321..47910117,3	K562	blood:
3	chr4:47908070..47910141-chr4:47912067..47913855,3	MCF-7	breast:
4	chr4:47901821..47910002-chr4:47912490..47917520,12	MCF-7	breast:
5	chr4:47899059..47902467-chr4:47904665..47908829,3	K562	blood:
6	chr4:47857858..47861058-chr4:47906882..47908675,3	MCF-7	breast:
7	chr4:47907905..47911619-chr4:47914071..47917997,8	K562	blood:
8	chr4:47892858..47894534-chr4:47908368..47910117,2	K562	blood:
9	chr4:47843029..47844670-chr4:47907030..47909401,2	K562	blood:
10	chr4:47905358..47911126-chr4:47914297..47917984,8	MCF-7	breast:
11	chr4:47906567..47911619-chr4:47914438..47917527,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163293	Chromatin interaction
ENSG00000170448	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10025104	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10030927	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10938503	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503789	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1440227	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1507922	0.82[EUR][1000 genomes]
rs1583808	0.86[ASN][1000 genomes]
rs16860723	0.90[ASN][1000 genomes]
rs2033897	0.86[ASN][1000 genomes]
rs2033898	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2053404	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289433	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2352145	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4529019	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694867	0.86[ASN][1000 genomes]
rs4694872	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695277	0.86[ASN][1000 genomes]
rs4695285	0.86[ASN][1000 genomes]
rs4695286	0.86[ASN][1000 genomes]
rs4695290	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4695292	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4695300	0.90[ASN][1000 genomes]
rs4695303	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695306	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4695307	0.89[ASN][1000 genomes]
rs4695308	0.89[ASN][1000 genomes]
rs57010305	0.90[ASN][1000 genomes]
rs58511183	0.90[ASN][1000 genomes]
rs60427744	0.90[ASN][1000 genomes]
rs60515154	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414687	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6447586	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6447592	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447593	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6811385	0.90[ASN][1000 genomes]
rs6816082	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6818556	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822668	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6827508	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6844286	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238638	0.85[ASN][1000 genomes]
rs73238639	0.86[ASN][1000 genomes]
rs73244433	0.86[ASN][1000 genomes]
rs73244436	0.88[ASN][1000 genomes]
rs73244437	0.89[ASN][1000 genomes]
rs73244438	0.90[ASN][1000 genomes]
rs73244439	0.90[ASN][1000 genomes]
rs73244442	0.86[ASN][1000 genomes]
rs7663935	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7687363	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7690562	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs920462	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9291317	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9683791	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

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

SNP	Gene	Cis/trans	Tissue	Source
rs1371730	CNGA1	cis	Heart Left Ventricle	GTEx
rs1371730	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	chr4:47876000-47915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:47876200-47915200	Weak transcription	Right Ventricle	heart
9	chr4:47876400-47915200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:47876800-47915800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:47877400-47913800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:47877600-47913600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:47877800-47910200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:47882200-47915200	Weak transcription	Stomach Mucosa	stomach
15	chr4:47882800-47913000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:47883200-47913600	Strong transcription	HMEC	breast
17	chr4:47883200-47913800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:47883200-47914400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:47884200-47913000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:47889800-47913400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:47890400-47913800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:47890400-47914200	Strong transcription	Liver	Liver
23	chr4:47890600-47909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:47890600-47910200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr4:47890800-47909600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:47890800-47913000	Strong transcription	Placenta	Placenta
27	chr4:47894600-47915200	Weak transcription	Aorta	Aorta
28	chr4:47894600-47915200	Weak transcription	Gastric	stomach
29	chr4:47895000-47913800	Weak transcription	Fetal Heart	heart
30	chr4:47896400-47912600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:47897800-47909800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr4:47898200-47909200	Weak transcription	Ovary	ovary
33	chr4:47898200-47915200	Weak transcription	Small Intestine	intestine
34	chr4:47898400-47915000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:47898400-47915200	Weak transcription	Colonic Mucosa	Colon
36	chr4:47898600-47915200	Weak transcription	Fetal Brain Male	brain
37	chr4:47899600-47915600	Weak transcription	Lung	lung
38	chr4:47899800-47915000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:47899800-47915200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:47899800-47915200	Weak transcription	Brain Substantia Nigra	brain
41	chr4:47900000-47908800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:47900000-47908800	Weak transcription	A549	lung
43	chr4:47900000-47909000	Weak transcription	NHEK	skin
44	chr4:47900000-47912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:47900000-47913800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr4:47900000-47914000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:47900000-47915200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:47900200-47915200	Weak transcription	HSMMtube	muscle
49	chr4:47900600-47915200	Weak transcription	Thymus	Thymus
50	chr4:47901000-47913600	Weak transcription	NHLF	lung

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