Variant report

Variant	rs12450227
Chromosome Location	chr17:63098626-63098627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:63098255..63100421-chr17:63117323..63119629,3	MCF-7	breast:
2	chr17:63094766..63097094-chr17:63098235..63100205,2	MCF-7	breast:
3	chr17:63051381..63054935-chr17:63092846..63100708,11	MCF-7	breast:
4	chr17:63097236..63098868-chr17:63102813..63104467,2	MCF-7	breast:
5	chr17:63051785..63054961-chr17:63094963..63102322,8	MCF-7	breast:
6	chr17:63098560..63101112-chr17:63116084..63117687,2	MCF-7	breast:
7	chr17:63097331..63099925-chr17:63102764..63104387,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263470	Chromatin interaction
ENSG00000120063	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11079556	0.86[EUR][1000 genomes]
rs11871788	0.97[ASN][1000 genomes]
rs12450951	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12453373	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12453609	0.99[ASN][1000 genomes]
rs1808918	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791236	0.95[ASN][1000 genomes]
rs62062507	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6504277	0.97[ASN][1000 genomes]
rs7215482	0.95[ASN][1000 genomes]
rs7225502	0.99[ASN][1000 genomes]
rs9892587	0.89[EUR][1000 genomes]
rs9903197	0.89[EUR][1000 genomes]
rs9908587	0.83[ASN][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	nsv1066765	chr17:62649313-63124303	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv530764	chr17:62939944-63278472	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv575872	chr17:63084995-63111452	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv112229	chr17:63095123-63104894	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:63097000-63102400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:63097200-63101000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:63097400-63101800	Weak transcription	Brain Germinal Matrix	brain
4	chr17:63097400-63102000	Weak transcription	Fetal Brain Male	brain
5	chr17:63097400-63102200	Weak transcription	NHLF	lung
6	chr17:63097400-63102400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:63097400-63102400	Weak transcription	Placenta	Placenta
8	chr17:63097400-63102600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:63097400-63112000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:63097600-63099200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr17:63097600-63099200	Weak transcription	Hela-S3	cervix
12	chr17:63097600-63099200	Weak transcription	HMEC	breast
13	chr17:63097600-63100400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr17:63097600-63101800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:63097600-63102000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr17:63097600-63102200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:63097600-63102200	Weak transcription	Brain Angular Gyrus	brain
18	chr17:63097600-63102200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr17:63097600-63102200	Weak transcription	Fetal Heart	heart
20	chr17:63097600-63102400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:63097600-63102400	Weak transcription	Fetal Kidney	kidney
22	chr17:63097600-63102400	Weak transcription	Right Atrium	heart
23	chr17:63097600-63102600	Weak transcription	Gastric	stomach
24	chr17:63097600-63102600	Weak transcription	Stomach Mucosa	stomach
25	chr17:63097600-63111800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr17:63097800-63099200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr17:63097800-63099200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:63097800-63099200	Weak transcription	GM12878-XiMat	blood
29	chr17:63097800-63099200	Weak transcription	NHEK	skin
30	chr17:63097800-63099400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:63097800-63099400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr17:63097800-63100400	Weak transcription	Colon Smooth Muscle	Colon
33	chr17:63097800-63100400	Weak transcription	Fetal Lung	lung
34	chr17:63097800-63100400	Weak transcription	Spleen	Spleen
35	chr17:63097800-63100600	Weak transcription	Brain Substantia Nigra	brain
36	chr17:63097800-63100600	Weak transcription	Esophagus	oesophagus
37	chr17:63097800-63100600	Weak transcription	Ovary	ovary
38	chr17:63097800-63100600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr17:63097800-63100600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr17:63097800-63100600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr17:63097800-63101000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr17:63097800-63101600	Weak transcription	Brain Anterior Caudate	brain
43	chr17:63097800-63101800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:63097800-63101800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr17:63097800-63101800	Weak transcription	Fetal Thymus	thymus
46	chr17:63097800-63101800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr17:63097800-63102000	Weak transcription	Adipose Nuclei	Adipose
48	chr17:63097800-63102000	Weak transcription	Brain Hippocampus Middle	brain
49	chr17:63097800-63102000	Weak transcription	Colonic Mucosa	Colon
50	chr17:63097800-63102000	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links