Variant report

Variant	rs28461523
Chromosome Location	chr4:6928605-6928606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:6926884..6928623-chr4:6939746..6942582,2	MCF-7	breast:
2	chr4:6917201..6921579-chr4:6924492..6930074,6	MCF-7	breast:
3	chr4:6909963..6912664-chr4:6925024..6930247,5	MCF-7	breast:
4	chr4:6926678..6929634-chr4:6988002..6989801,2	K562	blood:
5	chr4:6927493..6929739-chr4:6946981..6949624,2	K562	blood:
6	chr4:6928082..6930342-chr4:6930567..6933330,2	MCF-7	breast:
7	chr4:6927079..6929497-chr4:6940863..6942665,2	K562	blood:
8	chr4:6927466..6930094-chr4:7020098..7022400,2	MCF-7	breast:
9	chr4:6926678..6930436-chr4:6987384..6989801,3	K562	blood:
10	chr4:6925139..6926793-chr4:6927424..6929653,2	K562	blood:
11	chr4:6927079..6929042-chr4:6940771..6942363,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

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

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

rs_ID	r²[population]
rs10007838	1.00[AMR][1000 genomes]
rs10020561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10025944	1.00[AMR][1000 genomes]
rs10026013	1.00[AMR][1000 genomes]
rs13435398	1.00[AMR][1000 genomes]
rs13435488	1.00[AMR][1000 genomes]
rs28385367	1.00[AFR][1000 genomes]
rs28412715	1.00[AMR][1000 genomes]
rs28463590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28546580	1.00[AMR][1000 genomes]
rs28620599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28629411	1.00[AMR][1000 genomes]
rs28631659	1.00[AMR][1000 genomes]
rs28757648	1.00[AMR][1000 genomes]
rs73086431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73088550	1.00[AMR][1000 genomes]
rs9291119	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9994021	1.00[AMR][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	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6919600-6942200	Weak transcription	Hela-S3	cervix
2	chr4:6920200-6939600	Weak transcription	HUVEC	blood vessel
3	chr4:6920400-6931000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:6923200-6930800	Weak transcription	Stomach Mucosa	stomach
5	chr4:6924400-6930600	Weak transcription	Fetal Brain Male	brain
6	chr4:6924600-6929000	Strong transcription	Fetal Stomach	stomach
7	chr4:6925000-6928800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:6925400-6928800	Genic enhancers	Spleen	Spleen
9	chr4:6925800-6931400	Weak transcription	HSMMtube	muscle
10	chr4:6926000-6930600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:6926200-6930800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:6926200-6942000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:6926200-6942600	Weak transcription	NHEK	skin
14	chr4:6926200-6943200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:6926600-6928800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:6926600-6929600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr4:6926600-6930800	Weak transcription	Brain Angular Gyrus	brain
18	chr4:6926600-6930800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:6926600-6931000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:6926600-6932200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:6926600-6933400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr4:6926600-6935000	Enhancers	Liver	Liver
23	chr4:6926600-6939200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:6926800-6929600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:6926800-6930600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:6926800-6932200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr4:6927000-6929200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr4:6927000-6930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:6927200-6928800	Genic enhancers	GM12878-XiMat	blood
30	chr4:6927200-6929000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
31	chr4:6927200-6932200	Enhancers	Adipose Nuclei	Adipose
32	chr4:6927200-6932200	Genic enhancers	Thymus	Thymus
33	chr4:6927400-6929400	Weak transcription	Brain Germinal Matrix	brain
34	chr4:6927400-6929600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr4:6927400-6930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:6927600-6929000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:6927600-6931200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:6927600-6931600	Enhancers	Right Atrium	heart
39	chr4:6927600-6932200	Enhancers	Placenta	Placenta
40	chr4:6927800-6928800	Genic enhancers	Gastric	stomach
41	chr4:6927800-6929000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:6927800-6929600	Enhancers	Fetal Lung	lung
43	chr4:6927800-6929600	Enhancers	Small Intestine	intestine
44	chr4:6927800-6929600	Genic enhancers	K562	blood
45	chr4:6927800-6930000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:6927800-6930800	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:6927800-6931400	Genic enhancers	Fetal Intestine Small	intestine
48	chr4:6928000-6929000	Enhancers	Pancreas	Pancrea
49	chr4:6928000-6929200	Enhancers	Brain Hippocampus Middle	brain
50	chr4:6928000-6929600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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