Variant report

Variant	rs1497235
Chromosome Location	chr12:59160479-59160480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59145235..59147657-chr12:59160178..59163075,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11172711	1.00[ASN][1000 genomes]
rs11172727	1.00[JPT][hapmap]
rs1121270	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12367975	1.00[ASN][1000 genomes]
rs1391021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497236	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1531138	0.94[AFR][1000 genomes]
rs17121454	1.00[ASN][1000 genomes]
rs2124516	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605426	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645865	0.94[AFR][1000 genomes]
rs2645866	0.94[AFR][1000 genomes]
rs2645867	0.92[AFR][1000 genomes]
rs2712503	0.82[AFR][1000 genomes]
rs2712504	0.92[AFR][1000 genomes]
rs2712505	0.92[AFR][1000 genomes]
rs2712506	0.92[AFR][1000 genomes]
rs2712507	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2712508	0.94[AFR][1000 genomes]
rs2712510	0.95[AFR][1000 genomes]
rs2712511	0.94[AFR][1000 genomes]
rs2712513	0.92[AFR][1000 genomes]
rs2712514	0.92[AFR][1000 genomes]
rs2712515	0.97[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1049807	chr12:59069437-59227711	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv826390	chr12:59097995-59199786	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1497235	GTSF1	cis	cerebellum	SCAN
rs1497235	HOXC11	cis	cerebellum	SCAN
rs1497235	TSFM	cis	cerebellum	SCAN
rs1497235	RAB5B	cis	cerebellum	SCAN
rs1497235	CSAD	cis	cerebellum	SCAN
rs1497235	METTL1	cis	cerebellum	SCAN
rs1497235	ATP5B	cis	parietal	SCAN
rs1497235	SP7	cis	parietal	SCAN
rs1497235	OR6C4	cis	parietal	SCAN
rs1497235	IGFBP6	cis	parietal	SCAN
rs1497235	PCBP2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59157800-59162600	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr12:59158400-59160600	Enhancers	Rectal Smooth Muscle	rectum
3	chr12:59159000-59160800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr12:59159000-59160800	Enhancers	Stomach Mucosa	stomach
5	chr12:59159800-59160600	Enhancers	Fetal Intestine Small	intestine
6	chr12:59159800-59161000	Enhancers	Liver	Liver
7	chr12:59160000-59160800	Flanking Active TSS	HepG2	liver
8	chr12:59160400-59160600	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr12:59160400-59161600	Weak transcription	Ovary	ovary

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