Variant report

Variant	rs10055749
Chromosome Location	chr5:108023365-108023366
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	chr5:108021801..108024411-chr5:108062186..108064628,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272523	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10053099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10065015	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068485	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10072827	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477926	0.85[EUR][1000 genomes]
rs10477927	0.85[EUR][1000 genomes]
rs12332706	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13436390	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876624	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876625	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416193	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60052254	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6873702	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1024076	chr5:107991426-108028223	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv980959	chr5:108023194-108043010	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108007000-108034800	Weak transcription	Right Atrium	heart
2	chr5:108017600-108023600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:108017600-108023600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr5:108021000-108024000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr5:108021200-108024400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:108021200-108024600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr5:108021400-108024000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:108021400-108024200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:108021600-108024000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:108021800-108023600	Weak transcription	Osteobl	bone
11	chr5:108021800-108024000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:108021800-108024000	Enhancers	Fetal Brain Male	brain
13	chr5:108021800-108024200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr5:108022000-108023400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr5:108022000-108023400	Enhancers	Brain Cingulate Gyrus	brain
16	chr5:108022000-108024200	Enhancers	Brain Angular Gyrus	brain
17	chr5:108022000-108024400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr5:108022200-108023800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:108022200-108023800	Enhancers	Brain Anterior Caudate	brain
20	chr5:108022200-108024000	Enhancers	Brain Hippocampus Middle	brain
21	chr5:108022200-108024200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:108022400-108023800	Enhancers	Brain Germinal Matrix	brain
23	chr5:108022400-108024200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr5:108022400-108024400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr5:108022600-108023800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:108022600-108024400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr5:108022600-108024600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr5:108022800-108024400	Enhancers	Fetal Thymus	thymus
29	chr5:108023000-108024200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:108023000-108024400	Enhancers	GM12878-XiMat	blood
31	chr5:108023200-108023800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links