Variant report

Variant	rs12497559
Chromosome Location	chr3:150690018-150690019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12107625	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12107635	0.81[EUR][1000 genomes]
rs12485344	0.84[EUR][1000 genomes]
rs16863118	0.82[EUR][1000 genomes]
rs16863121	0.84[EUR][1000 genomes]
rs1876746	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434182	0.82[EUR][1000 genomes]
rs61104836	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62282747	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62282751	0.82[EUR][1000 genomes]
rs62282752	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62282753	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62284766	0.84[EUR][1000 genomes]
rs744669	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs744670	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7617623	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625786	0.81[EUR][1000 genomes]
rs7625985	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7647641	0.81[EUR][1000 genomes]

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	nsv915879	chr3:150607390-150860207	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr3:150685600-150690200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:150686800-150690600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:150687200-150690200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:150688000-150691000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:150688200-150691000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:150688600-150690800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:150688800-150690400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr3:150689000-150690200	Active TSS	Fetal Intestine Large	intestine
9	chr3:150689200-150690200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:150689200-150691000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:150689400-150690600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr3:150689400-150691000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:150689600-150691000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:150689800-150690200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:150689800-150691800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:150690000-150690200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:150690000-150690600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:150690000-150690800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:150690000-150690800	Active TSS	Duodenum Mucosa	Duodenum
20	chr3:150690000-150691000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:150690000-150694600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links