Variant report

Variant	rs1495850
Chromosome Location	chr1:227669682-227669683
allele	A/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	CTCF	chr1:227669660-227669810	HRPEpiC	eye:	n/a	n/a
2	RAD21	chr1:227669043-227669943	SK-N-SH	brain:	n/a	chr1:227669762-227669774
3	RAD21	chr1:227669215-227669694	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr1:227669250-227669758	MCF-7	breast:	n/a	n/a
5	CTCF	chr1:227669051-227669769	A549	lung:	n/a	n/a
6	RAD21	chr1:227669194-227669848	HCT-116	colon:	n/a	chr1:227669762-227669774
7	SMC3	chr1:227669145-227669843	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr1:227669133-227669777	H1-hESC	embryonic stem cell:	n/a	chr1:227669762-227669774
9	RAD21	chr1:227669212-227669835	HCT-116	colon:	n/a	chr1:227669762-227669774
10	RAD21	chr1:227669181-227669796	ECC-1	luminal epithelium:	n/a	chr1:227669762-227669774
11	MAFK	chr1:227669329-227670046	HepG2	liver:	n/a	chr1:227669811-227669825 chr1:227669810-227669826 chr1:227669808-227669828 chr1:227669813-227669828
12	MAFF	chr1:227669634-227669977	K562	blood:	n/a	chr1:227669812-227669830 chr1:227669811-227669825
13	ZNF263	chr1:227669302-227669728	HEK293-T-REx	kidney:	n/a	n/a
14	MAFK	chr1:227669599-227669971	HepG2	liver:	n/a	chr1:227669811-227669825 chr1:227669810-227669826 chr1:227669808-227669828 chr1:227669813-227669828
15	RAD21	chr1:227669169-227669756	A549	lung:	n/a	n/a
16	GATA3	chr1:227669534-227669827	SH-SY5Y	brain:	n/a	n/a
17	RAD21	chr1:227669171-227669703	H1-hESC	embryonic stem cell:	n/a	n/a
18	SMC3	chr1:227669238-227669701	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr1:227669052-227669869	SK-N-SH	brain:	n/a	n/a
20	SMC3	chr1:227669248-227669741	GM12878	blood:	n/a	n/a
21	RAD21	chr1:227669208-227669738	HepG2	liver:	n/a	n/a
22	RAD21	chr1:227669215-227669696	IMR90	lung:	n/a	n/a
23	RAD21	chr1:227669119-227669834	MCF-7	breast:	n/a	chr1:227669762-227669774
24	MAFK	chr1:227669313-227669964	K562	blood:	n/a	chr1:227669811-227669825 chr1:227669810-227669826 chr1:227669808-227669828 chr1:227669813-227669828
25	CTCF	chr1:227669214-227669687	GM12878	blood:	n/a	n/a
26	MAFK	chr1:227669396-227670003	IMR90	lung:	n/a	chr1:227669811-227669825 chr1:227669810-227669826 chr1:227669808-227669828 chr1:227669813-227669828
27	MAFK	chr1:227669358-227669934	H1-hESC	embryonic stem cell:	n/a	chr1:227669811-227669825 chr1:227669810-227669826 chr1:227669808-227669828 chr1:227669813-227669828
28	CEBPB	chr1:227669255-227669693	MCF-7	breast:	n/a	chr1:227669582-227669595
29	CTCF	chr1:227669206-227669905	HCT-116	colon:	n/a	n/a
30	MAFK	chr1:227669347-227669988	Hela-S3	cervix:	n/a	chr1:227669811-227669825 chr1:227669810-227669826 chr1:227669808-227669828 chr1:227669813-227669828
31	RAD21	chr1:227669155-227669829	A549	lung:	n/a	chr1:227669762-227669774
32	RAD21	chr1:227669202-227669724	ECC-1	luminal epithelium:	n/a	n/a
33	MAFF	chr1:227669428-227670026	HepG2	liver:	n/a	chr1:227669812-227669830 chr1:227669811-227669825
34	RAD21	chr1:227669232-227669739	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227669292..227669934-chr1:228141333..228142021,4	K562	blood:
2	chr1:227669242..227673785-chr1:227914780..227918377,5	MCF-7	breast:
3	chr1:227669109..227669887-chr1:228134058..228134849,3	K562	blood:
4	chr1:227668674..227670909-chr1:228132996..228135625,2	K562	blood:
5	chr1:227668984..227669861-chr1:228133992..228134634,2	MCF-7	breast:
6	chr1:227668951..227669884-chr1:227949577..227950975,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237193	TF binding region
ENSG00000143816	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10799414	1.00[JPT][hapmap]
rs10799420	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799421	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916130	1.00[JPT][hapmap]
rs10916148	0.81[AMR][1000 genomes]
rs10916150	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128670	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1390403	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2814086	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2819522	0.95[CEU][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2819524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000803	0.82[GIH][hapmap]
rs61833893	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61833894	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664147	0.91[GIH][hapmap];1.00[JPT][hapmap]
rs7549565	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875284	0.91[ASN][1000 genomes]
rs9628651	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1495850	OBSCN	cis	cerebellum	SCAN
rs1495850	ZNF678	cis	cerebellum	SCAN
rs1495850	CDC42BPA	cis	cerebellum	SCAN

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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