Variant report

Variant	rs911122
Chromosome Location	chr20:23625746-23625747
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	chr20:23615462..23617688-chr20:23624542..23627030,2	MCF-7	breast:
2	chr20:23610829..23612765-chr20:23625069..23626806,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2104006	0.83[EUR][1000 genomes]
rs2145233	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2145234	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2180663	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2424574	0.83[EUR][1000 genomes]
rs2424576	0.82[EUR][1000 genomes]
rs2424577	0.84[EUR][1000 genomes]
rs2424581	0.89[EUR][1000 genomes]
rs2424588	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2983603	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983604	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2983605	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2983640	1.00[ASW][hapmap]
rs62208871	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs726217	0.84[ASW][hapmap]

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	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs911122	CST3	cis	cerebellum	SCAN
rs911122	CST3	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618600-23626000	Weak transcription	Gastric	stomach
2	chr20:23618800-23626400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr20:23618800-23628600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr20:23622200-23636600	Weak transcription	Pancreas	Pancrea
5	chr20:23622800-23640000	Weak transcription	Stomach Mucosa	stomach
6	chr20:23623000-23634200	Weak transcription	Right Atrium	heart
7	chr20:23623200-23626800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:23623200-23636200	Weak transcription	Lung	lung
9	chr20:23623600-23626800	Weak transcription	NHEK	skin
10	chr20:23623600-23627200	Weak transcription	HMEC	breast
11	chr20:23623800-23626600	Weak transcription	HUVEC	blood vessel
12	chr20:23623800-23627000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:23624200-23633000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr20:23624400-23626600	Weak transcription	Fetal Muscle Leg	muscle
15	chr20:23624400-23627400	Weak transcription	HepG2	liver
16	chr20:23624600-23626800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr20:23624600-23633000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr20:23625000-23626000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:23625000-23626400	Weak transcription	Fetal Thymus	thymus
20	chr20:23625000-23626600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr20:23625000-23626600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr20:23625000-23627400	Enhancers	GM12878-XiMat	blood
23	chr20:23625000-23627600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr20:23625400-23626000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr20:23625600-23625800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr20:23625600-23626000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr20:23625600-23626800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links