Variant report

Variant	rs12500201
Chromosome Location	chr4:82395229-82395230
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	KAP1	chr4:82395098-82395579	HEK293	kidney:	n/a	n/a
2	FOXA2	chr4:82394857-82395333	A549	lung:	n/a	n/a
3	FOXA1	chr4:82395124-82395321	ECC-1	luminal epithelium:	n/a	n/a
4	FOXA1	chr4:82395056-82395331	T-47D	breast:	n/a	n/a
5	FOXA1	chr4:82395072-82395345	HepG2	liver:	n/a	n/a
6	YY1	chr4:82394921-82395399	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOXA1	chr4:82395038-82395337	T-47D	breast:	n/a	n/a
8	FOXA2	chr4:82395064-82395338	A549	lung:	n/a	n/a
9	FOXA2	chr4:82395072-82395261	HepG2	liver:	n/a	n/a
10	FOXA1	chr4:82395002-82395353	HepG2	liver:	n/a	n/a
11	FOXA1	chr4:82395093-82395272	HepG2	liver:	n/a	n/a
12	SETDB1	chr4:82395117-82395598	U2OS	brain:	n/a	n/a
13	MAFK	chr4:82395109-82395295	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
RASGEF1B	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10010140	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010394	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012642	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10015146	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10023826	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12502814	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102560	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13111699	1.00[ASN][1000 genomes]
rs13128387	0.90[ASN][1000 genomes]
rs13131664	0.95[ASN][1000 genomes]
rs16998600	0.97[ASN][1000 genomes]
rs17005142	1.00[ASN][1000 genomes]
rs17005144	1.00[ASN][1000 genomes]
rs17005145	1.00[ASN][1000 genomes]
rs28479652	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767523	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827174	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34128580	1.00[ASN][1000 genomes]
rs34749111	0.90[ASN][1000 genomes]
rs35010226	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35149381	0.95[ASN][1000 genomes]
rs35991185	1.00[ASN][1000 genomes]
rs36026752	1.00[ASN][1000 genomes]
rs41523946	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4693274	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693275	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693276	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693277	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62303604	1.00[ASN][1000 genomes]
rs6535252	1.00[ASN][1000 genomes]
rs6819741	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819989	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825177	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834665	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660392	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667427	0.81[AFR][1000 genomes]
rs7678464	0.90[ASN][1000 genomes]
rs7683852	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7684580	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688827	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7690069	0.95[ASN][1000 genomes]
rs7691170	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9307784	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][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	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829986	chr4:82345163-82509860	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82393800-82395400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:82393800-82395400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:82393800-82395400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:82393800-82395600	Enhancers	Gastric	stomach
5	chr4:82393800-82395800	Enhancers	Colon Smooth Muscle	Colon
6	chr4:82393800-82396000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:82393800-82396000	Enhancers	Stomach Mucosa	stomach
8	chr4:82394000-82395400	Enhancers	Placenta	Placenta
9	chr4:82394000-82396600	Weak transcription	Fetal Kidney	kidney
10	chr4:82394200-82395400	Enhancers	Primary B cells from peripheral blood	blood
11	chr4:82394400-82395400	Enhancers	Stomach Smooth Muscle	stomach
12	chr4:82394400-82395600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:82394400-82395800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:82394600-82395400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:82394600-82395400	Weak transcription	Colonic Mucosa	Colon
16	chr4:82394600-82395600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:82394600-82395600	Weak transcription	Esophagus	oesophagus
18	chr4:82394600-82395600	Enhancers	Lung	lung
19	chr4:82395200-82395400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr4:82395200-82395400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:82395200-82395600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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