Variant report

Variant	rs12488078
Chromosome Location	chr3:24519831-24519832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24517813..24520778-chr3:24535054..24537702,4	MCF-7	breast:
2	chr3:24513555..24516625-chr3:24517777..24521528,3	MCF-7	breast:
3	chr3:24516134..24523238-chr3:24531050..24538059,11	MCF-7	breast:
4	chr3:24518423..24520511-chr3:24527444..24530352,2	K562	blood:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12490491	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1865711	0.90[EUR][1000 genomes]
rs56783261	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58274299	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58388581	0.90[EUR][1000 genomes]
rs58932894	0.90[EUR][1000 genomes]
rs60502621	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61063562	0.90[EUR][1000 genomes]
rs6789815	0.98[ASN][1000 genomes]
rs73823308	0.95[EUR][1000 genomes]
rs73823340	0.89[AMR][1000 genomes];0.95[EUR][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	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24499600-24526800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:24509600-24531000	Weak transcription	Fetal Lung	lung
3	chr3:24515600-24533200	Weak transcription	Stomach Mucosa	stomach
4	chr3:24517200-24520400	Enhancers	Colon Smooth Muscle	Colon
5	chr3:24517400-24522600	Enhancers	Liver	Liver
6	chr3:24517800-24520600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:24517800-24521000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:24517800-24521000	Weak transcription	Pancreas	Pancrea
9	chr3:24517800-24521000	Weak transcription	HMEC	breast
10	chr3:24517800-24521200	Weak transcription	Aorta	Aorta
11	chr3:24517800-24521800	Weak transcription	Adipose Nuclei	Adipose
12	chr3:24517800-24523000	Weak transcription	Fetal Intestine Large	intestine
13	chr3:24517800-24523600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:24517800-24523800	Weak transcription	Gastric	stomach
15	chr3:24517800-24527000	Weak transcription	Lung	lung
16	chr3:24517800-24527000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:24517800-24527000	Weak transcription	Hela-S3	cervix
18	chr3:24517800-24528600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:24517800-24529000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:24518000-24521400	Weak transcription	NHEK	skin
21	chr3:24519000-24520400	Enhancers	H9 Cell Line	embryonic stem cell
22	chr3:24519000-24520600	Enhancers	Psoas Muscle	Psoas
23	chr3:24519200-24520000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
24	chr3:24519200-24521200	Weak transcription	Right Ventricle	heart
25	chr3:24519200-24521800	Weak transcription	HepG2	liver
26	chr3:24519200-24526800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:24519400-24520000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:24519400-24520400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr3:24519400-24520400	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:24519400-24520400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
31	chr3:24519400-24520400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
32	chr3:24519400-24520400	Weak transcription	Fetal Intestine Small	intestine
33	chr3:24519400-24521000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:24519400-24521200	Weak transcription	Left Ventricle	heart
35	chr3:24519400-24525200	Weak transcription	K562	blood
36	chr3:24519400-24525400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:24519400-24527400	Weak transcription	Right Atrium	heart
38	chr3:24519400-24532800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:24519600-24520200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
40	chr3:24519600-24520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:24519600-24521000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:24519600-24521400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:24519800-24520200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links