Variant report

Variant	rs2605426
Chromosome Location	chr12:59159191-59159192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11172711	1.00[ASN][1000 genomes]
rs11172727	1.00[JPT][hapmap]
rs1121270	0.97[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497235	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497236	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1531138	0.95[AFR][1000 genomes]
rs17121454	1.00[ASN][1000 genomes]
rs2124516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645865	0.95[AFR][1000 genomes]
rs2645866	0.95[AFR][1000 genomes]
rs2645867	0.94[AFR][1000 genomes]
rs2712503	0.84[AFR][1000 genomes]
rs2712504	0.94[AFR][1000 genomes]
rs2712505	0.94[AFR][1000 genomes]
rs2712506	0.94[AFR][1000 genomes]
rs2712507	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2712508	0.95[AFR][1000 genomes]
rs2712510	0.97[AFR][1000 genomes]
rs2712511	0.95[AFR][1000 genomes]
rs2712513	0.94[AFR][1000 genomes]
rs2712514	0.94[AFR][1000 genomes]
rs2712515	0.99[AFR][1000 genomes]
rs2712517	0.81[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
rs2605426	GTSF1	cis	cerebellum	SCAN
rs2605426	RAB5B	cis	cerebellum	SCAN
rs2605426	ATP5B	cis	parietal	SCAN
rs2605426	CSAD	cis	cerebellum	SCAN
rs2605426	TSFM	cis	cerebellum	SCAN
rs2605426	IGFBP6	cis	parietal	SCAN
rs2605426	OR6C4	cis	parietal	SCAN
rs2605426	SP7	cis	parietal	SCAN
rs2605426	METTL1	cis	cerebellum	SCAN
rs2605426	PCBP2	cis	cerebellum	SCAN
rs2605426	HOXC11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59153200-59159600	Enhancers	HepG2	liver
2	chr12:59154600-59160200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:59155800-59159200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:59156200-59159400	Enhancers	Liver	Liver
5	chr12:59156800-59160000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:59157600-59159200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:59157600-59159200	Enhancers	Fetal Intestine Small	intestine
8	chr12:59157800-59162600	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr12:59158200-59159200	Enhancers	NH-A	brain
10	chr12:59158200-59159200	Enhancers	NHLF	lung
11	chr12:59158200-59160200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:59158200-59160400	Enhancers	Colon Smooth Muscle	Colon
13	chr12:59158200-59160400	Enhancers	Ovary	ovary
14	chr12:59158400-59159400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:59158400-59159600	Weak transcription	HSMM	muscle
16	chr12:59158400-59160600	Enhancers	Rectal Smooth Muscle	rectum
17	chr12:59158600-59159800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:59158600-59160200	Weak transcription	Pancreas	Pancrea
19	chr12:59158800-59160400	Enhancers	Fetal Intestine Large	intestine
20	chr12:59159000-59160800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr12:59159000-59160800	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links