Variant report

Variant	rs28454329
Chromosome Location	chr3:141597853-141597854
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
2	chr3:141594674..141598943-chr3:141621711..141625603,5	MCF-7	breast:
3	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
4	chr3:141511387..141514014-chr3:141597034..141598647,2	K562	blood:
5	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:
6	chr3:141574992..141577884-chr3:141596784..141598377,2	K562	blood:

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction
ENSG00000114125	Chromatin interaction
ENSG00000200389	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11915071	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926859	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2068231	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2115938	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463227	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4511872	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58370035	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440048	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6767100	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6773662	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6782993	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6801868	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804938	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805115	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806440	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73230628	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7616510	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7624456	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642890	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648330	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849347	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853609	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3333253	chr3:141585303-141602936	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28454329	ATP1B3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141593400-141598000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:141593600-141598400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:141593800-141598000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:141593800-141598000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:141593800-141598000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:141593800-141598400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr3:141594000-141598000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr3:141594200-141598000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:141594200-141598000	Active TSS	Colonic Mucosa	Colon
10	chr3:141594400-141598000	Active TSS	Hela-S3	cervix
11	chr3:141594400-141600400	Active TSS	GM12878-XiMat	blood
12	chr3:141595600-141598400	Active TSS	Right Atrium	heart
13	chr3:141596000-141598000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:141596400-141598200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:141596400-141609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
17	chr3:141596600-141598000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:141596600-141598000	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr3:141596600-141598000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr3:141596600-141598400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr3:141596800-141598000	Flanking Active TSS	Thymus	Thymus
22	chr3:141596800-141598200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr3:141596800-141598200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr3:141597000-141598000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:141597000-141598000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr3:141597000-141598000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:141597000-141598000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr3:141597000-141598000	Enhancers	Fetal Lung	lung
29	chr3:141597000-141598200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:141597000-141598200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:141597000-141598200	Flanking Active TSS	HepG2	liver
32	chr3:141597000-141598200	Flanking Active TSS	HUVEC	blood vessel
33	chr3:141597000-141598400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr3:141597000-141598400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:141597000-141598400	Enhancers	Left Ventricle	heart
36	chr3:141597000-141598800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:141597000-141600400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:141597000-141604600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:141597000-141613200	Weak transcription	Placenta	Placenta
40	chr3:141597000-141615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:141597000-141625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:141597200-141598000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:141597200-141598000	Flanking Active TSS	Fetal Brain Female	brain
45	chr3:141597200-141598000	Enhancers	Fetal Heart	heart
46	chr3:141597200-141598000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:141597200-141598000	Flanking Active TSS	A549	lung
48	chr3:141597200-141598200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr3:141597200-141598200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:141597200-141598200	Flanking Active TSS	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links