Variant report

Variant	rs299824
Chromosome Location	chr17:63140687-63140688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:63137944..63140739-chr17:63146348..63148204,2	MCF-7	breast:
2	chr17:63118180..63120379-chr17:63138460..63140911,3	MCF-7	breast:
3	chr17:63133396..63138666-chr17:63139121..63145017,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108370	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1530351	0.90[CEU][hapmap]
rs1533336	0.81[CEU][hapmap]
rs167262	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007835	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2585860	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2585862	0.81[CEU][hapmap]
rs299821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes]
rs299822	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299823	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs299842	1.00[JPT][hapmap]
rs34821848	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414341	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs419526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438914	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446575	1.00[JPT][hapmap]
rs451403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
2	esv1009898	chr17:63135734-63146723	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:63134400-63143000	Weak transcription	Spleen	Spleen
2	chr17:63134400-63143200	Weak transcription	Esophagus	oesophagus
3	chr17:63134400-63169000	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:63135800-63146800	Weak transcription	Thymus	Thymus
5	chr17:63136000-63142800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:63138600-63151200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:63139400-63140800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:63139400-63143000	Weak transcription	GM12878-XiMat	blood
9	chr17:63139800-63140800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr17:63140000-63140800	Enhancers	Brain Angular Gyrus	brain
11	chr17:63140000-63140800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr17:63140000-63140800	Enhancers	Ovary	ovary
13	chr17:63140000-63140800	Bivalent Enhancer	NH-A	brain
14	chr17:63140000-63141000	Enhancers	Brain Cingulate Gyrus	brain
15	chr17:63140000-63141000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr17:63140000-63141200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr17:63140000-63141200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr17:63140200-63140800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:63140200-63140800	Weak transcription	Fetal Kidney	kidney
20	chr17:63140200-63142200	Enhancers	Fetal Thymus	thymus
21	chr17:63140400-63140800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr17:63140400-63140800	Bivalent Enhancer	K562	blood
23	chr17:63140400-63141000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:63140400-63141000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:63140400-63141000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr17:63140400-63142800	Weak transcription	Brain Hippocampus Middle	brain
27	chr17:63140600-63140800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:63140600-63140800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr17:63140600-63140800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr17:63140600-63140800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:63140600-63140800	Flanking Active TSS	Brain Substantia Nigra	brain
32	chr17:63140600-63140800	Enhancers	Gastric	stomach
33	chr17:63140600-63140800	Enhancers	Lung	lung
34	chr17:63140600-63140800	Enhancers	Right Atrium	heart
35	chr17:63140600-63141000	Enhancers	Brain Anterior Caudate	brain
36	chr17:63140600-63141200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links