Variant report

Variant	rs28665339
Chromosome Location	chr5:17316790-17316791
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:17247856..17249479-chr5:17315310..17317349,2	MCF-7	breast:
2	chr5:17315747..17318184-chr5:17334955..17337924,3	MCF-7	breast:
3	chr5:17216018..17220506-chr5:17315410..17318317,7	MCF-7	breast:
4	chr5:17301641..17309650-chr5:17311056..17318411,15	MCF-7	breast:
5	chr5:17216453..17223368-chr5:17315060..17319016,10	MCF-7	breast:
6	chr5:17315557..17317719-chr5:17358059..17359709,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185296	Chromatin interaction
ENSG00000176788	Chromatin interaction
ENSG00000215196	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10074496	0.81[ASN][1000 genomes]
rs10075136	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10462609	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11949223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13355635	0.81[ASN][1000 genomes]
rs16869688	0.94[ASN][1000 genomes]
rs16869690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1827400	0.81[ASN][1000 genomes]
rs28476505	0.81[ASN][1000 genomes]
rs56663279	0.81[ASN][1000 genomes]
rs56705013	0.81[ASN][1000 genomes]
rs58468495	0.81[ASN][1000 genomes]
rs6874823	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73052845	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73052871	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs73052881	0.81[ASN][1000 genomes]
rs73052887	0.81[ASN][1000 genomes]
rs73052888	0.81[ASN][1000 genomes]
rs73052898	0.81[ASN][1000 genomes]
rs73052901	0.81[ASN][1000 genomes]
rs7719794	0.81[ASN][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	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17307000-17317000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:17307000-17320200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:17314400-17318000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:17314800-17316800	Enhancers	Primary B cells from cord blood	blood
5	chr5:17314800-17317000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr5:17314800-17317200	Enhancers	Primary hematopoietic stem cells	blood
7	chr5:17315000-17316800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr5:17315000-17317400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:17315000-17318000	Enhancers	NHDF-Ad	bronchial
10	chr5:17315000-17318200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:17315000-17320800	Enhancers	Primary B cells from peripheral blood	blood
12	chr5:17315200-17316800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:17315200-17317600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:17315200-17318000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:17315200-17318000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr5:17315200-17318000	Enhancers	HMEC	breast
17	chr5:17315200-17318000	Enhancers	NHEK	skin
18	chr5:17315200-17318200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:17315200-17318200	Enhancers	NHLF	lung
20	chr5:17315400-17317000	Weak transcription	HSMM	muscle
21	chr5:17315400-17317200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:17315400-17317400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr5:17315400-17317800	Enhancers	Osteobl	bone
24	chr5:17315400-17318600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr5:17315600-17316800	Weak transcription	HSMMtube	muscle
26	chr5:17315600-17317000	Weak transcription	Brain Hippocampus Middle	brain
27	chr5:17315600-17318000	Enhancers	Adipose Nuclei	Adipose
28	chr5:17315600-17318400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr5:17315800-17316800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:17316000-17317000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:17316000-17317000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:17316000-17317000	Weak transcription	Fetal Lung	lung
33	chr5:17316000-17317000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr5:17316000-17317200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr5:17316000-17317200	Enhancers	Placenta	Placenta
36	chr5:17316000-17317200	Flanking Active TSS	GM12878-XiMat	blood
37	chr5:17316000-17317800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:17316000-17317800	Enhancers	NH-A	brain
39	chr5:17316000-17318000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:17316200-17317000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:17316200-17317000	Enhancers	Lung	lung
42	chr5:17316200-17317200	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr5:17316200-17317400	Enhancers	Stomach Mucosa	stomach
44	chr5:17316200-17317400	Flanking Active TSS	A549	lung
45	chr5:17316200-17317600	Enhancers	Duodenum Mucosa	Duodenum
46	chr5:17316200-17317800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:17316200-17318000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:17316200-17318000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:17316200-17319000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:17316400-17316800	Enhancers	Hela-S3	cervix

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