Variant report

Variant	rs1564651
Chromosome Location	chr5:16856257-16856258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16855463..16857293-chr5:16859556..16861090,2	MCF-7	breast:
2	chr5:16848554..16850179-chr5:16855617..16858396,2	K562	blood:
3	chr5:16854713..16857141-chr5:16861779..16864325,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1483015	0.98[AFR][1000 genomes]
rs253474	0.82[AFR][1000 genomes]
rs253475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs253477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59233189	1.00[AMR][1000 genomes]
rs7720898	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3529928	chr5:16748426-16856563	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3529929	chr5:16748426-16856563	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv1026773	chr5:16846836-16877367	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1034844	chr5:16854341-16903100	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 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	chr5:16839000-16864600	Weak transcription	Fetal Brain Female	brain
2	chr5:16842400-16862800	Weak transcription	Stomach Mucosa	stomach
3	chr5:16845600-16857000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:16852200-16856400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr5:16852400-16858200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:16853000-16856800	Weak transcription	Placenta	Placenta
7	chr5:16853000-16860600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:16853200-16856600	Weak transcription	Osteobl	bone
9	chr5:16853200-16857400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:16853400-16857000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr5:16853600-16858000	Enhancers	HSMMtube	muscle
12	chr5:16854000-16856600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:16854000-16859000	Weak transcription	Fetal Intestine Large	intestine
14	chr5:16854000-16862600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:16854600-16858000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:16854800-16858400	Enhancers	Fetal Muscle Leg	muscle
17	chr5:16855000-16857000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:16855000-16858000	Enhancers	NHDF-Ad	bronchial
19	chr5:16855000-16858200	Enhancers	NHLF	lung
20	chr5:16855000-16859000	Enhancers	Fetal Stomach	stomach
21	chr5:16855200-16856400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:16855200-16856800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:16855200-16857000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:16855200-16857400	Enhancers	HSMM	muscle
25	chr5:16855200-16858000	Weak transcription	Fetal Brain Male	brain
26	chr5:16855200-16858200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:16855200-16858800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:16855400-16856400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr5:16855400-16856400	Enhancers	Adipose Nuclei	Adipose
30	chr5:16855400-16856600	Enhancers	Fetal Lung	lung
31	chr5:16855600-16856400	Enhancers	Lung	lung
32	chr5:16855600-16856400	Genic enhancers	NHEK	skin
33	chr5:16855600-16856600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:16855600-16857000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr5:16855600-16857000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr5:16855600-16857200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:16855600-16857600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:16855600-16857800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:16855600-16858000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:16855600-16858000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:16855600-16858000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr5:16855600-16858200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:16855600-16858200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:16855600-16858800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:16855800-16856400	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr5:16855800-16857000	Enhancers	Spleen	Spleen
47	chr5:16855800-16857400	Enhancers	Esophagus	oesophagus
48	chr5:16855800-16857800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:16855800-16863000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:16856000-16857400	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links