Variant report

Variant	rs28409019
Chromosome Location	chr12:122030569-122030570
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	chr12:122014726..122017579-chr12:122028385..122031579,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089094	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10770191	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840649	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12320939	0.80[AFR][1000 genomes]
rs28651135	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28679490	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28758358	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934658	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6486789	0.80[AFR][1000 genomes]
rs7300349	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7397776	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7398628	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7399127	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122020800-122040400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:122021200-122036000	Weak transcription	Brain Germinal Matrix	brain
3	chr12:122021600-122033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:122028200-122031800	Enhancers	Placenta	Placenta
5	chr12:122028200-122038800	Weak transcription	Pancreas	Pancrea
6	chr12:122028600-122048000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:122028600-122048400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:122028800-122030600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:122028800-122030600	Enhancers	Fetal Thymus	thymus
10	chr12:122028800-122032000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:122028800-122032400	Weak transcription	Brain Anterior Caudate	brain
12	chr12:122028800-122033600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:122028800-122036000	Weak transcription	Fetal Intestine Small	intestine
14	chr12:122028800-122048400	Weak transcription	Brain Angular Gyrus	brain
15	chr12:122028800-122049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:122028800-122064000	Weak transcription	Right Atrium	heart
17	chr12:122029000-122030600	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:122029000-122033400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:122029200-122030600	Enhancers	Primary T cells from cord blood	blood
20	chr12:122029200-122030600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:122029200-122030600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:122029200-122030600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr12:122029200-122030600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr12:122029200-122030600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:122029200-122030600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:122029200-122030600	Enhancers	GM12878-XiMat	blood
27	chr12:122029200-122030800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:122029200-122030800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:122029200-122030800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:122029200-122030800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:122029200-122031200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr12:122029200-122031400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr12:122029200-122032000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:122029200-122032400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr12:122029200-122032400	Weak transcription	Brain Substantia Nigra	brain
36	chr12:122029200-122032800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:122029200-122032800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:122029200-122032800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:122029200-122032800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:122029200-122033600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:122029200-122033600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:122029200-122033600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:122029200-122033600	Weak transcription	K562	blood
44	chr12:122029200-122033800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:122029200-122034600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:122029200-122036200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr12:122029200-122036600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:122029200-122038000	Weak transcription	NHLF	lung
49	chr12:122029200-122038200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:122029200-122038800	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links