Variant report

Variant	rs1507922
Chromosome Location	chr4:47984429-47984430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:47984394-47984444	HRE	kidney:	n/a
2	chr4:47984394-47984444	AG04450	lung:	fetal
3	chr4:47984394-47984444	H1-hESC	embryonic stem cell:	embryo
4	chr4:47984394-47984444	GM06990	blood:	n/a
5	chr4:47984394-47984444	SKMC	muscle:	n/a
6	chr4:47984394-47984444	K562	blood:	n/a
7	chr4:47984394-47984444	AG04449	skin:	fetal
8	chr4:47984394-47984444	ECC-1	luminal epithelium:	n/a
9	chr4:47984394-47984444	U87	brain:	n/a
10	chr4:47984394-47984444	HEEpiC	esophagus:	n/a
11	chr4:47984394-47984444	LNCaP	prostate:	n/a
12	chr4:47984394-47984444	SK-N-SH	brain:	n/a
13	chr4:47984394-47984444	NB4	blood:	n/a
14	chr4:47984394-47984444	NT2-D1	testis:	n/a
15	chr4:47984394-47984444	HMEC	breast:	n/a
16	chr4:47984394-47984444	AG10803	skin:	n/a
17	chr4:47984394-47984444	BE2_C	brain:	n/a
18	chr4:47984394-47984444	PANC-1	pancreas:	n/a
19	chr4:47984394-47984444	SAEC	small airway:	n/a
20	chr4:47984394-47984444	MCF10A-Er-Src	breast:	n/a
21	chr4:47984394-47984444	HAEpiC	amniotic membrane:	n/a
22	chr4:47984394-47984444	GM19239	blood:	n/a
23	chr4:47984394-47984444	GM12891	blood:	n/a
24	chr4:47984394-47984444	HNPCEpiC	eye:	n/a
25	chr4:47984394-47984444	IMR90	lung:	fetal
26	chr4:47984394-47984444	SK-N-SH_RA	brain:	n/a
27	chr4:47984394-47984444	PFSK-1	brain:	n/a
28	chr4:47984394-47984444	HCT-116	colon:	n/a
29	chr4:47984394-47984444	GM12892	blood:	n/a
30	chr4:47984394-47984444	T-47D	breast:	n/a
31	chr4:47984394-47984444	HUVEC	blood vessel:	n/a
32	chr4:47984394-47984444	HIPEpiC	eye:	n/a
33	chr4:47984394-47984444	ovcar-3	ovarian:	n/a
34	chr4:47984394-47984444	BJ	skin:	n/a
35	chr4:47984394-47984444	ProgFib	skin:	n/a
36	chr4:47984394-47984444	Hela-S3	cervix:	n/a
37	chr4:47984394-47984444	SK-N-MC	brain:	n/a
38	chr4:47984394-47984444	GM12878	blood:	n/a
39	chr4:47984394-47984444	HPAEpiC	pulmonary alveolar:	n/a
40	chr4:47984394-47984444	AG09319	gingival:	n/a
41	chr4:47984394-47984444	HCM	heart:	n/a
42	chr4:47984394-47984444	HepG2	liver:	n/a
43	chr4:47984394-47984444	HL-60	blood:	n/a
44	chr4:47984394-47984444	CMK	blood:	n/a
45	chr4:47984394-47984444	NHDF-neo	bronchial:	n/a
46	chr4:47984394-47984444	NH-A	brain:	n/a
47	chr4:47984394-47984444	HRPEpiC	eye:	n/a
48	chr4:47984394-47984444	HCPEpiC	choroid plexus:	n/a
49	chr4:47984394-47984444	A549	lung:	n/a
50	chr4:47984394-47984444	Caco-2	colon:	n/a

No data

Variant related genes	Relation type
CNGA1	CpG island

Extended variants
information (count: 110 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10002498	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs10020447	0.90[GIH][hapmap];0.81[TSI][hapmap]
rs10025104	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs10030927	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs10938503	0.86[EUR][1000 genomes]
rs10938515	0.93[ASN][1000 genomes]
rs10938516	0.91[CHB][hapmap]
rs11733284	0.88[JPT][hapmap]
rs11736427	0.88[JPT][hapmap]
rs11944982	0.88[ASN][1000 genomes]
rs12503789	0.92[EUR][1000 genomes]
rs13116684	0.87[GIH][hapmap]
rs13120847	0.88[JPT][hapmap]
rs13146880	0.88[JPT][hapmap]
rs1348023	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs1371730	0.82[EUR][1000 genomes]
rs1440227	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs1507920	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1550444	0.90[GIH][hapmap];0.81[TSI][hapmap]
rs1583808	0.94[CHB][hapmap]
rs167692	0.97[GIH][hapmap]
rs16860723	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs16860815	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1961011	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1972883	0.90[GIH][hapmap];0.82[TSI][hapmap]
rs2033895	0.90[GIH][hapmap];0.81[TSI][hapmap]
rs2033897	0.94[CHB][hapmap];0.92[CHD][hapmap]
rs2033898	0.84[EUR][1000 genomes]
rs2053404	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs2053408	0.93[ASN][1000 genomes]
rs2289433	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs2352145	0.88[EUR][1000 genomes]
rs3113878	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs321622	0.88[JPT][hapmap]
rs321630	0.88[JPT][hapmap]
rs321631	0.88[JPT][hapmap]
rs321632	0.87[GIH][hapmap]
rs321636	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321638	0.90[ASN][1000 genomes]
rs321643	0.93[ASN][1000 genomes]
rs321645	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3762858	0.90[GIH][hapmap];0.82[TSI][hapmap]
rs3762859	0.90[GIH][hapmap];0.82[TSI][hapmap]
rs4365692	0.90[GIH][hapmap];0.81[TSI][hapmap]
rs4518215	0.87[ASN][1000 genomes]
rs4529019	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs4694867	0.94[CHB][hapmap]
rs4694868	0.90[GIH][hapmap]
rs4694871	0.90[GIH][hapmap];0.81[TSI][hapmap]
rs4694872	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs4695285	0.94[CHB][hapmap]
rs4695286	0.94[CHB][hapmap]
rs4695287	0.86[GIH][hapmap];0.81[TSI][hapmap]
rs4695290	0.84[EUR][1000 genomes]
rs4695292	0.86[EUR][1000 genomes]
rs4695300	0.94[CHB][hapmap]
rs4695303	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs4695306	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs4695307	1.00[CHB][hapmap]
rs4695309	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs4695321	0.85[ASN][1000 genomes]
rs59936075	0.87[ASN][1000 genomes]
rs60515154	0.91[EUR][1000 genomes]
rs61654183	0.84[ASN][1000 genomes]
rs6414687	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs6447586	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs6447592	0.89[EUR][1000 genomes]
rs6447593	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs6447601	0.87[ASN][1000 genomes]
rs6447605	0.88[ASN][1000 genomes]
rs6447606	0.85[ASN][1000 genomes]
rs6447608	0.83[ASN][1000 genomes]
rs6811385	0.94[CHB][hapmap]
rs6816082	0.91[EUR][1000 genomes]
rs6816153	0.83[ASN][1000 genomes]
rs6818556	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs6822668	0.86[EUR][1000 genomes]
rs6827508	0.94[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs6829073	0.87[GIH][hapmap]
rs6829804	0.88[ASN][1000 genomes]
rs6832334	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs6832503	0.88[JPT][hapmap]
rs6833320	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs6838837	0.93[ASN][1000 genomes]
rs6839185	0.84[ASN][1000 genomes]
rs6841271	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs6844286	0.90[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs6854375	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs73244450	0.87[ASN][1000 genomes]
rs73244455	0.92[ASN][1000 genomes]
rs73244464	0.88[ASN][1000 genomes]
rs73244465	0.86[ASN][1000 genomes]
rs73244466	0.87[ASN][1000 genomes]
rs73244467	0.88[ASN][1000 genomes]
rs7663935	0.85[EUR][1000 genomes]
rs7667811	0.85[ASN][1000 genomes]
rs7687363	0.86[EUR][1000 genomes]
rs7690103	0.88[ASN][1000 genomes]
rs7690562	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs893864	0.90[GIH][hapmap]
rs920462	0.86[EUR][1000 genomes]
rs9291317	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][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	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
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013163	chr4:47977844-48022511	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537084	chr4:47977844-48022511	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1507922	CNGA1	cis	Thyroid	GTEx
rs1507922	CNGA1	cis	Muscle Skeletal	GTEx
rs1507922	CNGA1	cis	Adipose Subcutaneous	GTEx
rs1507922	CNGA1	cis	Esophagus Muscularis	GTEx
rs1507922	CNGA1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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