Variant report

Variant	rs6453208
Chromosome Location	chr5:75464430-75464431
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	chr5:75464408-75464458	AG09309	skin:	n/a
2	chr5:75464408-75464458	Caco-2	colon:	n/a
3	chr5:75464408-75464458	GM19239	blood:	n/a
4	chr5:75464408-75464458	HMEC	breast:	n/a
5	chr5:75464408-75464458	HEK293	kidney:	embryo
6	chr5:75464408-75464458	SK-N-MC	brain:	n/a
7	chr5:75464408-75464458	BJ	skin:	n/a
8	chr5:75464408-75464458	T-47D	breast:	n/a
9	chr5:75464408-75464458	K562	blood:	n/a
10	chr5:75464408-75464458	HCF	heart:	n/a
11	chr5:75464408-75464458	HCPEpiC	choroid plexus:	n/a
12	chr5:75464408-75464458	LNCaP	prostate:	n/a
13	chr5:75464408-75464458	HRPEpiC	eye:	n/a
14	chr5:75464408-75464458	HEEpiC	esophagus:	n/a
15	chr5:75464408-75464458	SKMC	muscle:	n/a
16	chr5:75464408-75464458	PANC-1	pancreas:	n/a
17	chr5:75464408-75464458	PFSK-1	brain:	n/a
18	chr5:75464408-75464458	AG10803	skin:	n/a
19	chr5:75464408-75464458	HRE	kidney:	n/a
20	chr5:75464408-75464458	SK-N-SH_RA	brain:	n/a
21	chr5:75464408-75464458	IMR90	lung:	fetal
22	chr5:75464408-75464458	PrEC	prostate:	n/a
23	chr5:75464408-75464458	Jurkat	blood:	n/a
24	chr5:75464408-75464458	ProgFib	skin:	n/a
25	chr5:75464408-75464458	HL-60	blood:	n/a
26	chr5:75464408-75464458	MCF10A-Er-Src	breast:	n/a
27	chr5:75464408-75464458	AG04449	skin:	fetal
28	chr5:75464408-75464458	U87	brain:	n/a
29	chr5:75464408-75464458	HUVEC	blood vessel:	n/a
30	chr5:75464408-75464458	NH-A	brain:	n/a
31	chr5:75464408-75464458	HRCEpiC	kidney:	n/a
32	chr5:75464408-75464458	ECC-1	luminal epithelium:	n/a
33	chr5:75464408-75464458	NB4	blood:	n/a
34	chr5:75464408-75464458	GM12878	blood:	n/a
35	chr5:75464408-75464458	NT2-D1	testis:	n/a
36	chr5:75464408-75464458	ovcar-3	ovarian:	n/a
37	chr5:75464408-75464458	GM12891	blood:	n/a
38	chr5:75464408-75464458	GM12892	blood:	n/a
39	chr5:75464408-75464458	HPAEpiC	pulmonary alveolar:	n/a
40	chr5:75464408-75464458	AG04450	lung:	fetal
41	chr5:75464408-75464458	SK-N-SH	brain:	n/a
42	chr5:75464408-75464458	HepG2	liver:	n/a
43	chr5:75464408-75464458	GM06990	blood:	n/a
44	chr5:75464408-75464458	NHDF-neo	bronchial:	n/a
45	chr5:75464408-75464458	Hela-S3	cervix:	n/a
46	chr5:75464408-75464458	AG09319	gingival:	n/a
47	chr5:75464408-75464458	MCF-7	breast:	n/a
48	chr5:75464408-75464458	BE2_C	brain:	n/a
49	chr5:75464408-75464458	RPTEC	kidney:	n/a
50	chr5:75464408-75464458	H1-hESC	embryonic stem cell:	embryo

No data

Variant related genes	Relation type
ENSG00000251668	CpG island

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1002541	0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10038253	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10039662	0.91[ASN][1000 genomes]
rs10040232	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064352	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10066377	0.89[CEU][hapmap]
rs10474464	0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10514062	0.80[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10942755	0.85[YRI][hapmap]
rs11742697	0.84[CEU][hapmap]
rs12152728	0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12153073	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12153396	0.84[CHD][hapmap]
rs12522434	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12522618	0.89[CEU][hapmap]
rs12655684	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12657276	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1393224	1.00[JPT][hapmap]
rs1423106	0.83[CHD][hapmap]
rs1423107	0.84[CHD][hapmap]
rs1553324	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1553325	0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1895390	0.89[CEU][hapmap]
rs2055439	0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2194177	0.84[CHD][hapmap]
rs2358531	0.80[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs4493648	0.93[ASN][1000 genomes]
rs4532342	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4582256	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4610441	0.89[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs4703696	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4703697	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4704283	0.96[CEU][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4704284	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4704285	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4704286	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58628146	0.89[EUR][1000 genomes]
rs6414966	0.90[ASN][1000 genomes]
rs6414967	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6414968	0.98[EUR][1000 genomes]
rs6414969	0.84[ASN][1000 genomes]
rs6866404	0.85[CEU][hapmap]
rs6868505	0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6873987	0.81[YRI][hapmap]
rs7445798	0.91[ASN][1000 genomes]
rs7448148	0.91[ASN][1000 genomes]
rs7710307	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7719752	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7723492	0.85[YRI][hapmap]
rs7732173	0.88[GIH][hapmap]
rs7732692	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9293675	0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1034853	chr5:75382047-75534981	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv462212	chr5:75388834-75534570	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv598676	chr5:75388834-75534570	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv526084	chr5:75410511-75530494	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv2757119	chr5:75426863-75474780	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv2759351	chr5:75426863-75474780	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv34958	chr5:75429015-75474921	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6453208	AP3B1	cis	cerebellum	SCAN
rs6453208	FCHO2	cis	parietal	SCAN
rs6453208	METTL7A	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75461200-75465200	Weak transcription	Brain Anterior Caudate	brain

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