Variant report

Variant	rs28658139
Chromosome Location	chr17:20811999-20812000
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	chr17:20811890..20812833-chr21:33785672..33786611,2	Hela-S3	cervix:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs6587105	1.00[EUR][1000 genomes]
rs73313035	1.00[EUR][1000 genomes]
rs73313051	1.00[EUR][1000 genomes]
rs9891613	1.00[EUR][1000 genomes]
rs9902929	1.00[EUR][1000 genomes]
rs9904375	1.00[EUR][1000 genomes]
rs9910047	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9913944	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv3361931	chr17:20539962-20845258	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv3330516	chr17:20572433-20862663	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv574597	chr17:20802778-20872331	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20801800-20812200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:20810000-20812800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr17:20810200-20812600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:20811200-20812000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr17:20811200-20812200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr17:20811200-20812200	Active TSS	Colonic Mucosa	Colon
7	chr17:20811200-20812200	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr17:20811200-20812200	Active TSS	Hela-S3	cervix
9	chr17:20811200-20812200	Active TSS	K562	blood
10	chr17:20811200-20812400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:20811200-20812400	Active TSS	Stomach Smooth Muscle	stomach
12	chr17:20811400-20812000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:20811400-20812000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr17:20811400-20812000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:20811400-20812000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr17:20811400-20812000	Active TSS	Osteobl	bone
17	chr17:20811400-20812200	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr17:20811400-20812200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr17:20811400-20812200	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr17:20811400-20812200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:20811400-20812200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr17:20811400-20812200	Active TSS	Brain Angular Gyrus	brain
23	chr17:20811400-20812200	Active TSS	Brain Cingulate Gyrus	brain
24	chr17:20811400-20812200	Active TSS	Brain Hippocampus Middle	brain
25	chr17:20811400-20812200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr17:20811400-20812200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr17:20811400-20812200	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr17:20811400-20812200	Active TSS	Fetal Stomach	stomach
29	chr17:20811400-20812200	Active TSS	Pancreas	Pancrea
30	chr17:20811400-20812200	Active TSS	Rectal Smooth Muscle	rectum
31	chr17:20811400-20812200	Active TSS	NHDF-Ad	bronchial
32	chr17:20811400-20812400	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr17:20811400-20812400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr17:20811400-20812400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr17:20811400-20812400	Active TSS	Fetal Brain Female	brain
36	chr17:20811400-20812400	Active TSS	Fetal Intestine Small	intestine
37	chr17:20811400-20812400	Active TSS	Psoas Muscle	Psoas
38	chr17:20811400-20812400	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr17:20811400-20812400	Active TSS	Right Ventricle	heart
40	chr17:20811400-20812400	Enhancers	Small Intestine	intestine
41	chr17:20811400-20812600	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr17:20811400-20812600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:20811400-20812600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:20811400-20812600	Active TSS	Brain Anterior Caudate	brain
45	chr17:20811400-20812600	Enhancers	Fetal Heart	heart
46	chr17:20811400-20812600	Active TSS	Fetal Lung	lung
47	chr17:20811400-20812600	Flanking Active TSS	NHEK	skin
48	chr17:20811600-20812000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr17:20811600-20812000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr17:20811600-20812000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links