Variant report

Variant	rs4704283
Chromosome Location	chr5:75470816-75470817
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr5:75470808-75471380	HCT-116	colon:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
2	RAD21	chr5:75470785-75471356	ECC-1	luminal epithelium:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
3	RAD21	chr5:75470768-75471366	MCF-7	breast:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
4	CTCF	chr5:75470763-75471313	MCF-7	breast:	n/a	chr5:75471073-75471082 chr5:75471062-75471083 chr5:75471067-75471085
5	RAD21	chr5:75470790-75471297	HepG2	liver:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
6	SMC3	chr5:75470802-75471333	GM12878	blood:	n/a	chr5:75471069-75471083
7	WRNIP1	chr5:75470719-75471163	GM12878	blood:	n/a	n/a
8	CTCF	chr5:75470778-75471206	K562	blood:	n/a	chr5:75471073-75471082 chr5:75471062-75471083 chr5:75471067-75471085
9	RAD21	chr5:75470752-75471204	H1-hESC	embryonic stem cell:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
10	RAD21	chr5:75470772-75471204	SK-N-SH_RA	brain:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
11	CTCF	chr5:75470750-75472090	SK-N-SH	brain:	n/a	chr5:75471073-75471082 chr5:75471062-75471083 chr5:75471067-75471085
12	RAD21	chr5:75470806-75471339	ECC-1	luminal epithelium:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
13	MXI1	chr5:75470592-75472288	SK-N-SH	brain:	n/a	n/a
14	RAD21	chr5:75470807-75471380	HCT-116	colon:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
15	RAD21	chr5:75470782-75471204	H1-hESC	embryonic stem cell:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
16	CTCF	chr5:75470510-75471444	A549	lung:	n/a	chr5:75471073-75471082 chr5:75471062-75471083 chr5:75471067-75471085
17	SMC3	chr5:75470650-75472048	SK-N-SH	brain:	n/a	chr5:75471069-75471083
18	RAD21	chr5:75470813-75471350	A549	lung:	n/a	chr5:75471065-75471084 chr5:75471069-75471083
19	CTCF	chr5:75470736-75471320	HCT-116	colon:	n/a	chr5:75471073-75471082 chr5:75471062-75471083 chr5:75471067-75471085
20	RAD21	chr5:75470386-75472489	SK-N-SH	brain:	n/a	chr5:75471065-75471084 chr5:75471069-75471083 chr5:75471450-75471462
21	GATA2	chr5:75470570-75472089	SH-SY5Y	brain:	n/a	chr5:75471846-75471863 chr5:75471841-75471857 chr5:75470627-75470643 chr5:75471845-75471854 chr5:75471844-75471854
22	CTCF	chr5:75470800-75471291	MCF-7	breast:	n/a	chr5:75471073-75471082 chr5:75471062-75471083 chr5:75471067-75471085

No.	Distal block	Cell Line	Cell type
1	chr5:75370002..75370997-chr5:75470399..75471572,8	MCF-7	breast:
2	chr5:75370258..75370917-chr5:75470691..75471438,2	MCF-7	breast:
3	chr5:75470625..75471456-chr5:75551799..75552684,5	MCF-7	breast:
4	chr5:75182130..75182669-chr5:75470688..75471450,3	MCF-7	breast:
5	chr5:75030911..75031730-chr5:75470555..75471416,3	MCF-7	breast:
6	chr5:75031130..75031721-chr5:75470748..75471418,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254893	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10038253	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040232	0.80[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10064352	0.80[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10066377	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10474464	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514060	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10514061	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10514062	0.93[GIH][hapmap];1.00[LWK][hapmap]
rs11742697	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12152728	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522434	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522618	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13153946	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13155330	1.00[CHB][hapmap]
rs13158110	0.87[ASN][1000 genomes]
rs13174339	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs13178459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1553324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553325	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565925	1.00[CHB][hapmap]
rs17565946	1.00[CHB][hapmap]
rs17565960	1.00[CHB][hapmap]
rs17650942	1.00[CHB][hapmap]
rs17651115	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs17651281	1.00[JPT][hapmap]
rs1895390	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2055439	0.80[ASW][hapmap]
rs2358531	0.93[GIH][hapmap];1.00[LWK][hapmap]
rs34476924	1.00[ASN][1000 genomes]
rs35357454	0.81[ASN][1000 genomes]
rs4532342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582256	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610441	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs4703696	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703697	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704284	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704286	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58628146	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62361382	0.87[ASN][1000 genomes]
rs62363488	0.87[ASN][1000 genomes]
rs62363490	0.87[ASN][1000 genomes]
rs6414967	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414968	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453205	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs6453206	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6453208	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]
rs6859434	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6860159	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6866404	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6881418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs72771998	0.81[ASN][1000 genomes]
rs736005	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7701465	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7710307	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718358	1.00[CHB][hapmap]
rs7719752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732173	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7732692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734441	0.81[ASN][1000 genomes]
rs9293675	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	esv989228	chr5:75466097-75470949	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4704283	METTL7A	trans	cerebellum	SCAN
rs4704283	FCHO2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75470600-75471200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:75470600-75472200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr5:75470600-75472600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:75470600-75472800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:75470600-75476400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:75470800-75471200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr5:75470800-75471400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:75470800-75472600	Enhancers	Primary B cells from peripheral blood	blood

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