Variant report

Variant	rs17573709
Chromosome Location	chr4:47955758-47955759
allele	C/T
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	chr4:47955755-47955805	GM06990	blood:	n/a
2	chr4:47955755-47955805	AG04449	skin:	fetal
3	chr4:47955755-47955805	T-47D	breast:	n/a
4	chr4:47955755-47955805	HEEpiC	esophagus:	n/a
5	chr4:47955755-47955805	HMEC	breast:	n/a
6	chr4:47955755-47955805	HCPEpiC	choroid plexus:	n/a
7	chr4:47955755-47955805	Caco-2	colon:	n/a
8	chr4:47955755-47955805	SK-N-SH_RA	brain:	n/a
9	chr4:47955755-47955805	HCF	heart:	n/a
10	chr4:47955755-47955805	A549	lung:	n/a
11	chr4:47955755-47955805	HRE	kidney:	n/a
12	chr4:47955755-47955805	GM12878	blood:	n/a
13	chr4:47955755-47955805	K562	blood:	n/a
14	chr4:47955755-47955805	HepG2	liver:	n/a
15	chr4:47955755-47955805	GM12891	blood:	n/a
16	chr4:47955755-47955805	SK-N-MC	brain:	n/a
17	chr4:47955755-47955805	PANC-1	pancreas:	n/a
18	chr4:47955755-47955805	HUVEC	blood vessel:	n/a
19	chr4:47955755-47955805	SKMC	muscle:	n/a
20	chr4:47955755-47955805	PFSK-1	brain:	n/a
21	chr4:47955755-47955805	ECC-1	luminal epithelium:	n/a
22	chr4:47955755-47955805	AG04450	lung:	fetal
23	chr4:47955755-47955805	NT2-D1	testis:	n/a
24	chr4:47955755-47955805	LNCaP	prostate:	n/a
25	chr4:47955755-47955805	Hela-S3	cervix:	n/a
26	chr4:47955755-47955805	HRCEpiC	kidney:	n/a
27	chr4:47955755-47955805	ProgFib	skin:	n/a
28	chr4:47955755-47955805	HIPEpiC	eye:	n/a
29	chr4:47955755-47955805	NHBE	bronchial:	n/a
30	chr4:47955755-47955805	HNPCEpiC	eye:	n/a
31	chr4:47955755-47955805	HAEpiC	amniotic membrane:	n/a
32	chr4:47955755-47955805	MCF-7	breast:	n/a
33	chr4:47955755-47955805	NHDF-neo	bronchial:	n/a
34	chr4:47955755-47955805	Jurkat	blood:	n/a
35	chr4:47955755-47955805	HCM	heart:	n/a
36	chr4:47955755-47955805	HRPEpiC	eye:	n/a
37	chr4:47955755-47955805	GM12892	blood:	n/a
38	chr4:47955755-47955805	BJ	skin:	n/a
39	chr4:47955755-47955805	HPAEpiC	pulmonary alveolar:	n/a
40	chr4:47955755-47955805	IMR90	lung:	fetal
41	chr4:47955755-47955805	H1-hESC	embryonic stem cell:	embryo
42	chr4:47955755-47955805	AG09309	skin:	n/a
43	chr4:47955755-47955805	BE2_C	brain:	n/a
44	chr4:47955755-47955805	Hepatocyte	liver:	n/a
45	chr4:47955755-47955805	HL-60	blood:	n/a
46	chr4:47955755-47955805	GM19239	blood:	n/a
47	chr4:47955755-47955805	SK-N-SH	brain:	n/a
48	chr4:47955755-47955805	SAEC	small airway:	n/a
49	chr4:47955755-47955805	U87	brain:	n/a
50	chr4:47955755-47955805	MCF10A-Er-Src	breast:	n/a

No data

Variant related genes	Relation type
CNGA1	CpG island

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10008818	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs10028155	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10049713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1012844	0.85[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1062858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10938499	0.82[EUR][1000 genomes]
rs10938500	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10938504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10938505	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10938506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12186152	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12504018	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12506632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12507439	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12510002	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12641871	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12651301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1371729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1371731	0.90[EUR][1000 genomes]
rs1371732	0.81[YRI][hapmap]
rs1440228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17463666	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1822030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1866689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1984713	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2289435	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2352470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28395298	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28412313	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28460483	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28573115	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28583602	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28636596	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4435717	0.83[EUR][1000 genomes]
rs4565052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56001837	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6447587	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6447589	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6811177	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6823184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6823698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs6833758	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6858440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8180146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs978094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9994561	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9995122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9997555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv967291	chr4:47954000-47981934	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17573709	RP11-121C2.2	cis	Whole Blood	GTEx
rs17573709	NFXL1	cis	Whole Blood	GTEx
rs17573709	CORIN	cis	Whole Blood	GTEx
rs17573709	CNGA1	cis	cerebellum	SCAN
rs17573709	TNFRSF1A	trans	lymphoblastoid	seeQTL
rs17573709	CNGA1	cis	Muscle Skeletal	GTEx
rs17573709	CNGA1	cis	Thyroid	GTEx
rs17573709	CNGA1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47954600-47959200	Weak transcription	Right Atrium	heart

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