Variant report

Variant	rs28781570
Chromosome Location	chr12:123948106-123948107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123942949..123945032-chr12:123947880..123951007,3	MCF-7	breast:
2	chr12:123947470..123950375-chr12:124015636..124018854,3	K562	blood:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction
ENSG00000184209	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11497310	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11507743	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11516174	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11516175	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11516178	0.88[EUR][1000 genomes]
rs11522341	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11522342	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11522343	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11523309	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11535679	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13303358	0.87[EUR][1000 genomes]
rs28493578	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28703907	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28728075	0.87[EUR][1000 genomes]
rs28894691	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61953496	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7957839	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9697330	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9697415	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9697423	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9723026	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9723244	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9777715	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9777830	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123943600-123949200	Weak transcription	Ovary	ovary
2	chr12:123943600-123955800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123943800-123949000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:123943800-123949000	Weak transcription	Osteobl	bone
5	chr12:123943800-123949200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:123943800-123949200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:123943800-123949200	Weak transcription	Adipose Nuclei	Adipose
8	chr12:123943800-123949200	Weak transcription	Fetal Heart	heart
9	chr12:123943800-123949200	Weak transcription	Fetal Kidney	kidney
10	chr12:123943800-123949200	Weak transcription	Gastric	stomach
11	chr12:123943800-123949200	Weak transcription	NH-A	brain
12	chr12:123943800-123949400	Weak transcription	Brain Anterior Caudate	brain
13	chr12:123943800-123949400	Weak transcription	HSMM	muscle
14	chr12:123943800-123949600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:123943800-123949600	Weak transcription	Aorta	Aorta
16	chr12:123943800-123949600	Weak transcription	Brain Angular Gyrus	brain
17	chr12:123943800-123949600	Weak transcription	Esophagus	oesophagus
18	chr12:123943800-123949800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:123943800-123949800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:123943800-123949800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:123943800-123949800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:123943800-123949800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:123943800-123949800	Weak transcription	Left Ventricle	heart
24	chr12:123943800-123949800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:123943800-123949800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:123943800-123949800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:123943800-123949800	Weak transcription	Right Ventricle	heart
28	chr12:123943800-123956000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:123943800-123956400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:123943800-123958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:123943800-123959600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:123943800-123959600	Weak transcription	Psoas Muscle	Psoas
33	chr12:123943800-123961200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:123944000-123948200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr12:123944000-123949000	Weak transcription	Placenta	Placenta
36	chr12:123944000-123949200	Weak transcription	Fetal Brain Female	brain
37	chr12:123944000-123949200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:123944000-123949200	Weak transcription	NHLF	lung
39	chr12:123944000-123949600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:123944000-123949800	Weak transcription	HMEC	breast
41	chr12:123944000-123950200	Weak transcription	HSMMtube	muscle
42	chr12:123944200-123949000	Weak transcription	Fetal Intestine Large	intestine
43	chr12:123944200-123949600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:123944200-123949600	Weak transcription	Colonic Mucosa	Colon
45	chr12:123944200-123949800	Weak transcription	Lung	lung
46	chr12:123944200-123949800	Weak transcription	Pancreas	Pancrea
47	chr12:123944400-123949200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:123944400-123949200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:123944400-123949200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:123944400-123949200	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links