Variant report

Variant	rs6478025
Chromosome Location	chr9:99994643-99994644
allele	C/G
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	EP300	chr9:99994345-99994837	HepG2	liver:	n/a	n/a
2	RCOR1	chr9:99994599-99994993	K562	blood:	n/a	n/a
3	CBX3	chr9:99994472-99995102	K562	blood:	n/a	n/a
4	FOXA1	chr9:99994307-99994865	HepG2	liver:	n/a	chr9:99994576-99994591
5	TAL1	chr9:99994518-99995018	K562	blood:	n/a	n/a
6	HDAC2	chr9:99994486-99994785	HepG2	liver:	n/a	n/a
7	CEBPB	chr9:99994509-99994781	A549	lung:	n/a	chr9:99994608-99994619
8	SP1	chr9:99994304-99994923	A549	lung:	n/a	n/a
9	NR3C1	chr9:99994477-99994670	A549	lung:	n/a	n/a
10	MYC	chr9:99994426-99994701	MCF10A-Er-Src	breast:	n/a	chr9:99994570-99994580
11	FOXA2	chr9:99994374-99994975	A549	lung:	n/a	n/a
12	NR2F2	chr9:99994431-99995001	K562	blood:	n/a	n/a
13	MAX	chr9:99994417-99994954	K562	blood:	n/a	chr9:99994570-99994580
14	TRIM28	chr9:99994375-99995116	K562	blood:	n/a	n/a
15	FOXA2	chr9:99994327-99994885	A549	lung:	n/a	n/a
16	CEBPD	chr9:99994407-99995152	K562	blood:	n/a	n/a
17	STAT5A	chr9:99994467-99995072	K562	blood:	n/a	n/a
18	GATA3	chr9:99994470-99994754	A549	lung:	n/a	n/a
19	POLR2A	chr9:99994614-99995021	K562	blood:	n/a	n/a
20	TEAD4	chr9:99994478-99995109	K562	blood:	n/a	n/a
21	SP1	chr9:99994415-99994820	HepG2	liver:	n/a	n/a
22	TEAD4	chr9:99994485-99995111	K562	blood:	n/a	n/a
23	STAT5A	chr9:99994492-99995105	K562	blood:	n/a	n/a
24	CEBPB	chr9:99994430-99994777	A549	lung:	n/a	chr9:99994608-99994619
25	FOXA1	chr9:99994417-99994798	HepG2	liver:	n/a	chr9:99994576-99994591
26	CEBPB	chr9:99994400-99994971	K562	blood:	n/a	chr9:99994608-99994619
27	FOXA2	chr9:99994429-99994774	HepG2	liver:	n/a	n/a
28	CEBPB	chr9:99994424-99994811	K562	blood:	n/a	chr9:99994608-99994619
29	MYC	chr9:99994496-99994900	K562	blood:	n/a	chr9:99994570-99994580
30	FOXA1	chr9:99994428-99994806	HepG2	liver:	n/a	chr9:99994576-99994591
31	FOXA1	chr9:99994411-99994812	HepG2	liver:	n/a	chr9:99994576-99994591
32	MAX	chr9:99994507-99994811	A549	lung:	n/a	chr9:99994570-99994580
33	MAX	chr9:99994521-99994797	A549	lung:	n/a	chr9:99994570-99994580
34	KAP1	chr9:99994436-99994721	U2OS	brain:	n/a	n/a
35	TEAD4	chr9:99994338-99994843	HepG2	liver:	n/a	n/a
36	NR3C1	chr9:99994390-99995153	A549	lung:	n/a	n/a
37	MYC	chr9:99994430-99994701	MCF10A-Er-Src	breast:	n/a	chr9:99994570-99994580
38	NR2F2	chr9:99994292-99995098	K562	blood:	n/a	n/a
39	CEBPB	chr9:99994431-99994716	HepG2	liver:	n/a	chr9:99994608-99994619
40	POLR2A	chr9:99994634-99995182	H1-hESC	embryonic stem cell:	n/a	n/a
41	NR3C1	chr9:99994299-99994905	A549	lung:	n/a	n/a
42	FOSL2	chr9:99994432-99994688	HepG2	liver:	n/a	n/a
43	CEBPB	chr9:99994520-99994739	A549	lung:	n/a	chr9:99994608-99994619
44	GATA2	chr9:99994419-99995175	K562	blood:	n/a	n/a
45	SP1	chr9:99994269-99994902	A549	lung:	n/a	n/a
46	MYC	chr9:99994441-99994841	K562	blood:	n/a	chr9:99994570-99994580

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:99994043..99996478-chr9:99999503..100002032,3	K562	blood:

Variant related genes	Relation type
ENSG00000235494	TF binding region
ENSG00000254483	Chromatin interaction
ENSG00000197816	Chromatin interaction
ENSG00000203279	Chromatin interaction
ENSG00000254876	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10125824	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759521	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10759526	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817273	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12685723	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7858579	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6478025	VN1R51P	cis	Thyroid	GTEx
rs6478025	CCDC180	cis	Artery Tibial	GTEx
rs6478025	RP11-498P14.5	cis	lung	GTEx
rs6478025	RP11-498P14.5	cis	Thyroid	GTEx
rs6478025	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs6478025	ANKRD18CP	cis	Thyroid	GTEx
rs6478025	RP11-520B13.4	cis	Thyroid	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99985200-99995000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:99985800-99994800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:99992200-99999600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:99993400-99995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:99994000-99995800	Enhancers	K562	blood
6	chr9:99994200-99995600	Enhancers	HepG2	liver
7	chr9:99994200-99995800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:99994400-99994800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr9:99994400-99995000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:99994400-99995000	Weak transcription	A549	lung
11	chr9:99994400-99995400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:99994400-99995600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr9:99994600-99994800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr9:99994600-99995000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:99994600-99998200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:99994600-99998400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links