Variant report

Variant	rs3105789
Chromosome Location	chr5:90228431-90228432
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90224688..90232317-chr5:90673389..90680405,10	MCF-7	breast:
2	chr5:90226329..90230726-chr5:90675433..90680039,8	MCF-7	breast:
3	chr5:90228093..90228615-chr5:90680787..90681318,2	MCF-7	breast:
4	chr5:90227817..90228486-chr5:90521512..90522261,2	MCF-7	breast:
5	chr5:90226670..90228954-chr5:90237004..90239086,2	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10057134	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942618	0.92[CEU][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942619	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744005	0.96[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749470	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750515	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163934	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967413	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2063244	0.91[CEU][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2367182	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3105790	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3114653	0.90[AFR][1000 genomes]
rs3114655	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4415111	0.96[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452914	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867530	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705201	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716083	0.85[AMR][1000 genomes];0.89[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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats 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	58 gene(s)	inside rSNPs	diseases
2	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90208000-90231000	Weak transcription	Brain Anterior Caudate	brain
2	chr5:90225600-90229600	Weak transcription	Placenta	Placenta
3	chr5:90225600-90232400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:90225800-90230200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:90225800-90236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:90225800-90244000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:90226200-90228800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:90226600-90230600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr5:90226600-90230800	Enhancers	HepG2	liver
10	chr5:90226800-90229400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr5:90226800-90229600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:90226800-90229800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr5:90227000-90228600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:90227200-90229000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:90227200-90229200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:90227200-90229600	Weak transcription	K562	blood
17	chr5:90227200-90230000	Enhancers	A549	lung
18	chr5:90227800-90229200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr5:90227800-90229400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:90227800-90229800	Enhancers	Fetal Kidney	kidney
21	chr5:90228000-90228600	Enhancers	Liver	Liver
22	chr5:90228000-90229000	Weak transcription	Fetal Stomach	stomach
23	chr5:90228000-90229800	Enhancers	Colon Smooth Muscle	Colon
24	chr5:90228200-90228600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:90228200-90229800	Enhancers	Fetal Heart	heart
26	chr5:90228200-90230400	Enhancers	Stomach Mucosa	stomach
27	chr5:90228400-90228600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:90228400-90229200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:90228400-90229600	Weak transcription	Fetal Intestine Large	intestine
30	chr5:90228400-90239200	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links