Variant report

Variant	rs473706
Chromosome Location	chr7:99424751-99424752
allele	C/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	GATA3	chr7:99424524-99426205	MCF-7	breast:	n/a	chr7:99425893-99425904 chr7:99425892-99425900
2	USF1	chr7:99424683-99425140	HepG2	liver:	n/a	chr7:99424894-99424905
3	POLR2A	chr7:99424319-99424846	HepG2	liver:	n/a	n/a
4	HEY1	chr7:99424502-99424955	HepG2	liver:	n/a	n/a
5	TEAD4	chr7:99424664-99426074	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:99424460-99424912	HepG2	liver:	n/a	n/a
7	NFIC	chr7:99424463-99425675	HepG2	liver:	n/a	n/a
8	MBD4	chr7:99424639-99425286	HepG2	liver:	n/a	n/a
9	FOXA2	chr7:99424696-99426131	HepG2	liver:	n/a	n/a
10	NFIC	chr7:99424628-99425332	HepG2	liver:	n/a	n/a
11	FOXA1	chr7:99424737-99425374	A549	lung:	n/a	n/a
12	FOXA1	chr7:99424643-99426060	HepG2	liver:	n/a	n/a
13	FOXA1	chr7:99424643-99426058	HepG2	liver:	n/a	n/a
14	MYBL2	chr7:99424540-99425971	HepG2	liver:	n/a	n/a
15	SP1	chr7:99424606-99425671	HepG2	liver:	n/a	n/a
16	POLR2A	chr7:99424679-99424886	HepG2	liver:	n/a	n/a
17	FOXA1	chr7:99424658-99426061	HepG2	liver:	n/a	n/a
18	GATA3	chr7:99424604-99426143	MCF-7	breast:	n/a	chr7:99425893-99425904 chr7:99425892-99425900
19	USF1	chr7:99424723-99424989	HepG2	liver:	n/a	chr7:99424894-99424905
20	MAX	chr7:99424560-99425370	HepG2	liver:	n/a	n/a
21	TCF12	chr7:99424633-99425564	MCF-7	breast:	n/a	chr7:99425435-99425444
22	EP300	chr7:99424635-99425513	HepG2	liver:	n/a	n/a
23	CEBPB	chr7:99424745-99425340	MCF-7	breast:	n/a	chr7:99424982-99424993
24	EP300	chr7:99424599-99425438	HepG2	liver:	n/a	n/a
25	SIN3AK20	chr7:99424534-99426163	MCF-7	breast:	n/a	n/a
26	HDAC2	chr7:99424690-99425393	MCF-7	breast:	n/a	n/a
27	POLR2A	chr7:99423282-99425951	MCF10A-Er-Src	breast:	n/a	n/a
28	MYBL2	chr7:99424533-99425333	HepG2	liver:	n/a	n/a
29	CEBPB	chr7:99424688-99425458	MCF-7	breast:	n/a	chr7:99424982-99424993
30	NR2F2	chr7:99424621-99425916	HepG2	liver:	n/a	n/a
31	POLR2A	chr7:99424606-99424963	HepG2	liver:	n/a	n/a
32	TBP	chr7:99424720-99425125	HepG2	liver:	n/a	n/a
33	BHLHE40	chr7:99424742-99425120	HepG2	liver:	n/a	n/a
34	HDAC2	chr7:99424680-99425230	HepG2	liver:	n/a	n/a
35	MYC	chr7:99424726-99425370	MCF10A-Er-Src	breast:	n/a	n/a
36	NR2F2	chr7:99424696-99425480	MCF-7	breast:	n/a	n/a
37	FOXA2	chr7:99424729-99426033	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99412647..99414218-chr7:99422343..99425321,2	K562	blood:
2	chr7:99213826..99215884-chr7:99424650..99426774,2	MCF-7	breast:

Variant related genes	Relation type
CYP3A43	TF binding region
ENSG00000197037	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17161786	1.00[TSI][hapmap]
rs2687095	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2687102	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2687103	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs493380	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs496000	0.81[LWK][hapmap]
rs663495	0.83[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827709	chr7:99353500-99440051	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs473706	AP4M1	cis	lymphoblastoid	seeQTL
rs473706	COPS6	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99419400-99432200	Enhancers	Fetal Intestine Small	intestine
2	chr7:99419600-99432000	Enhancers	Fetal Intestine Large	intestine
3	chr7:99420600-99424800	Enhancers	Pancreas	Pancrea
4	chr7:99420600-99425200	Enhancers	HepG2	liver
5	chr7:99421000-99425800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr7:99421000-99426400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr7:99422800-99437400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:99423800-99426600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr7:99424000-99426600	Weak transcription	Adipose Nuclei	Adipose
10	chr7:99424200-99425400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:99424200-99430400	Enhancers	K562	blood
12	chr7:99424400-99426600	Enhancers	Stomach Mucosa	stomach
13	chr7:99424600-99425400	Enhancers	Liver	Liver
14	chr7:99424600-99425400	Enhancers	Hela-S3	cervix
15	chr7:99424600-99426000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:99424600-99429200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links