Variant report

Variant	rs12072789
Chromosome Location	chr1:209380482-209380483
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	chr1:209379971..209382311-chr1:209606603..209608628,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11119236	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11119243	1.00[AMR][1000 genomes]
rs11119246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11119249	1.00[AMR][1000 genomes]
rs11119250	1.00[AMR][1000 genomes]
rs12067172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12071550	1.00[AMR][1000 genomes]
rs12073260	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12076575	1.00[AMR][1000 genomes]
rs12077614	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12079171	1.00[AMR][1000 genomes]
rs12079883	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080089	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12081438	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088612	1.00[AMR][1000 genomes]
rs12095589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12096528	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12354318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9782963	1.00[AMR][1000 genomes]
rs9782983	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209370400-209380800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209373200-209380800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:209373200-209381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:209377000-209380600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:209377000-209380800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:209377200-209381200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:209377400-209380800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:209377600-209380600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:209379000-209380600	Weak transcription	Fetal Lung	lung
10	chr1:209380000-209380800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
11	chr1:209380200-209380800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:209380200-209380800	Enhancers	Fetal Brain Male	brain
13	chr1:209380200-209380800	Enhancers	Fetal Brain Female	brain
14	chr1:209380200-209381200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
15	chr1:209380400-209380600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:209380400-209380600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:209380400-209380600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:209380400-209380600	Enhancers	Brain Anterior Caudate	brain
19	chr1:209380400-209380600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:209380400-209380600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
21	chr1:209380400-209380600	Enhancers	Fetal Stomach	stomach
22	chr1:209380400-209380800	Enhancers	Brain Germinal Matrix	brain
23	chr1:209380400-209380800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr1:209380400-209380800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr1:209380400-209380800	Enhancers	Ovary	ovary
26	chr1:209380400-209380800	Bivalent Enhancer	Right Ventricle	heart
27	chr1:209380400-209381000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:209380400-209381200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:209380400-209381400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:209380400-209381400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:209380400-209381800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links