Variant report

Variant	rs28553332
Chromosome Location	chr3:141548197-141548198
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141455754..141459793-chr3:141546409..141549893,5	MCF-7	breast:
2	chr3:141548195..141550715-chr3:141563735..141566666,2	K562	blood:
3	chr3:141546349..141549180-chr3:141595509..141597123,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11569266	1.00[ASN][1000 genomes]
rs2060014	1.00[ASN][1000 genomes]
rs66789997	1.00[ASN][1000 genomes]
rs67167142	1.00[ASN][1000 genomes]
rs9818297	1.00[ASN][1000 genomes]
rs9821680	1.00[ASN][1000 genomes]
rs9839365	1.00[ASN][1000 genomes]
rs9876068	1.00[ASN][1000 genomes]
rs9876627	1.00[ASN][1000 genomes]
rs9883557	1.00[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	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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141544800-141550800	Weak transcription	Right Atrium	heart
2	chr3:141546000-141548200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:141546200-141548400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:141546400-141548400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:141547000-141548200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:141547000-141548200	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr3:141547000-141548200	Enhancers	K562	blood
8	chr3:141547000-141548400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:141547000-141548400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:141547000-141549000	Enhancers	NHEK	skin
11	chr3:141547000-141550600	Enhancers	Hela-S3	cervix
12	chr3:141547200-141548200	Enhancers	Fetal Muscle Leg	muscle
13	chr3:141547200-141548200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr3:141547200-141548400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr3:141547200-141548400	Enhancers	HSMMtube	muscle
16	chr3:141547200-141548600	Enhancers	Placenta	Placenta
17	chr3:141547200-141548800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:141547200-141549400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:141547200-141550000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:141547200-141550600	Enhancers	HMEC	breast
21	chr3:141547600-141548200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:141547600-141548200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:141547600-141548200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr3:141547600-141548200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:141547600-141548200	Enhancers	Fetal Intestine Small	intestine
26	chr3:141547600-141548600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr3:141547800-141548200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:141547800-141548200	Enhancers	Adipose Nuclei	Adipose
29	chr3:141547800-141548200	Enhancers	Esophagus	oesophagus
30	chr3:141547800-141548200	Enhancers	Fetal Muscle Trunk	muscle
31	chr3:141547800-141548200	Enhancers	Left Ventricle	heart
32	chr3:141547800-141548200	Enhancers	Lung	lung
33	chr3:141547800-141548200	Enhancers	Pancreas	Pancrea
34	chr3:141547800-141548200	Enhancers	Psoas Muscle	Psoas
35	chr3:141547800-141548200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr3:141547800-141548400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:141548000-141548200	Flanking Active TSS	HSMM	muscle
38	chr3:141548000-141548400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:141548000-141550400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:141548000-141550800	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links