Variant report

Variant	rs3762536
Chromosome Location	chr2:10089722-10089723
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	POLR2A	chr2:10089694-10090054	HepG2	liver:	n/a	n/a
2	FOXA1	chr2:10089511-10089899	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:10089517-10090007	HepG2	liver:	n/a	n/a
4	MYBL2	chr2:10089527-10090185	HepG2	liver:	n/a	n/a
5	MAX	chr2:10089602-10092724	HepG2	liver:	n/a	n/a
6	FOXA2	chr2:10089666-10089882	HepG2	liver:	n/a	n/a
7	SP1	chr2:10089584-10090024	HepG2	liver:	n/a	n/a
8	FOXA1	chr2:10089516-10089988	HepG2	liver:	n/a	n/a
9	ARID3A	chr2:10089715-10089811	HepG2	liver:	n/a	n/a
10	MAX	chr2:10089567-10092486	HepG2	liver:	n/a	n/a
11	RXRA	chr2:10089602-10089940	HepG2	liver:	n/a	chr2:10089874-10089890 chr2:10089764-10089777 chr2:10089764-10089777
12	MYBL2	chr2:10089480-10090031	HepG2	liver:	n/a	n/a
13	HEY1	chr2:10089688-10090113	HepG2	liver:	n/a	n/a
14	FOXA1	chr2:10089574-10089998	HepG2	liver:	n/a	n/a
15	HNF4A	chr2:10089671-10090023	HepG2	liver:	n/a	chr2:10089764-10089778 chr2:10089765-10089777
16	HNF4A	chr2:10089680-10090006	HepG2	liver:	n/a	chr2:10089764-10089778 chr2:10089765-10089777
17	YY1	chr2:10089677-10090155	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10086473..10090081-chr2:10090865..10093730,3	MCF-7	breast:
2	chr2:9982092..9985559-chr2:10088577..10093200,6	MCF-7	breast:
3	chr2:9962243..9964669-chr2:10088779..10091216,2	MCF-7	breast:
4	chr2:10085922..10087593-chr2:10089321..10091253,3	K562	blood:

Variant related genes	Relation type
GRHL1	TF binding region
ENSG00000134317	Chromatin interaction
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1001215	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12616347	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12618788	0.87[MEX][hapmap];0.89[TSI][hapmap]
rs13009358	0.99[ASN][1000 genomes]
rs1864539	0.87[MEX][hapmap]
rs2033324	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033325	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34629102	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35321554	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35646916	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35816086	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762538	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828260	0.85[CEU][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4669508	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669511	0.85[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72784422	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784424	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72784425	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891500	0.85[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3762536	CYS1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10082000-10090800	Weak transcription	HMEC	breast
2	chr2:10082400-10090200	Weak transcription	Gastric	stomach
3	chr2:10082600-10090400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:10084600-10089800	Weak transcription	Lung	lung
5	chr2:10084800-10090200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:10085200-10089800	Weak transcription	Hela-S3	cervix
7	chr2:10085800-10090600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:10086000-10090800	Weak transcription	Pancreas	Pancrea
9	chr2:10086200-10090800	Weak transcription	Right Atrium	heart
10	chr2:10086400-10089800	Weak transcription	Esophagus	oesophagus
11	chr2:10088200-10090000	Weak transcription	Placenta	Placenta
12	chr2:10088800-10089800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:10088800-10090800	Enhancers	Spleen	Spleen
14	chr2:10089000-10090000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:10089600-10090200	Flanking Active TSS	HepG2	liver

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