Variant report

Variant	rs1009289
Chromosome Location	chr1:151475540-151475541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	1:151411623-151426875..1:151473324-151476039	H1-hESC	embryonic stem cell:	embryo
2	chr1:151444312..151446471-chr1:151475179..151477134,2	MCF-7	breast:
3	chr1:151459917..151461603-chr1:151473316..151475793,2	K562	blood:
4	chr1:151474013..151475617-chr1:151966742..151969004,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229021	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000143442	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10127622	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10788807	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788808	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888418	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888419	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204834	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204835	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204837	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11204838	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11204839	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11583133	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12026585	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032983	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037100	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12118440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128578	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730114	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1547832	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573129	0.80[ASN][1000 genomes]
rs1573130	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2211435	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298167	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2298168	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2337359	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61261719	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6675984	0.83[ASN][1000 genomes]
rs7548090	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552458	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151468400-151476600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:151468400-151482400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:151468600-151482400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:151470200-151482400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:151471000-151476600	Enhancers	Fetal Intestine Small	intestine
6	chr1:151474000-151475800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:151474000-151475800	Enhancers	K562	blood
8	chr1:151474200-151476200	Enhancers	HepG2	liver
9	chr1:151474400-151476200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:151474400-151476200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:151474400-151477000	Enhancers	Fetal Intestine Large	intestine
12	chr1:151474600-151475800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:151474600-151475800	Enhancers	Hela-S3	cervix
14	chr1:151475000-151476200	Enhancers	Fetal Lung	lung
15	chr1:151475000-151477000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:151475200-151475800	Enhancers	Pancreas	Pancrea
17	chr1:151475200-151475800	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr1:151475200-151475800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr1:151475200-151476000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:151475200-151476000	Enhancers	Colonic Mucosa	Colon
21	chr1:151475200-151477200	Weak transcription	Small Intestine	intestine
22	chr1:151475400-151475800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:151475400-151475800	Enhancers	A549	lung
24	chr1:151475400-151476200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:151475400-151476600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:151475400-151481600	Weak transcription	Stomach Mucosa	stomach
27	chr1:151475400-151481800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:151475400-151483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links