Variant report

Variant	rs28407629
Chromosome Location	chr15:79275466-79275467
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:79275397..79277408-chr15:79277642..79280073,2	MCF-7	breast:
2	chr15:79275375..79276949-chr15:79288666..79290515,2	MCF-7	breast:
3	chr15:79164464..79167320-chr15:79273608..79277179,4	K562	blood:
4	chr15:79264746..79267610-chr15:79273645..79276620,3	K562	blood:
5	chr15:79274591..79277278-chr15:79290967..79292503,2	K562	blood:
6	chr15:79264746..79267610-chr15:79274625..79276620,2	K562	blood:
7	chr15:79274407..79277285-chr15:79277913..79280154,2	K562	blood:
8	chr15:79165092..79167959-chr15:79271269..79275481,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction
ENSG00000058335	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12101364	1.00[EUR][1000 genomes]
rs16970387	0.81[EUR][1000 genomes]
rs28368520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28391216	1.00[EUR][1000 genomes]
rs28427472	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28461937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28513164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28516885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28546944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28547879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28549817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28557276	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28565526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28567804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28603308	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28624404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28674868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28683537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28709904	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28716558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28718997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28722773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28738778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920807	1.00[AMR][1000 genomes];0.91[EUR][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	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904433	chr15:79243571-79310288	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79244000-79288000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:79261200-79280400	Weak transcription	Esophagus	oesophagus
3	chr15:79270000-79278400	Weak transcription	Fetal Intestine Small	intestine
4	chr15:79271400-79275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:79271600-79275800	Weak transcription	Lung	lung
6	chr15:79272200-79275600	Weak transcription	Brain Angular Gyrus	brain
7	chr15:79272200-79275600	Weak transcription	Right Ventricle	heart
8	chr15:79272200-79275800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:79272200-79275800	Weak transcription	Placenta	Placenta
10	chr15:79272200-79275800	Weak transcription	Right Atrium	heart
11	chr15:79272200-79276000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:79272200-79276000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:79272200-79276200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:79272200-79280000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:79272200-79280000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:79272200-79280200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:79272200-79280200	Weak transcription	Pancreas	Pancrea
18	chr15:79272200-79280400	Weak transcription	Brain Substantia Nigra	brain
19	chr15:79272200-79280600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:79272200-79284400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:79272400-79275800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:79272400-79279600	Weak transcription	Fetal Intestine Large	intestine
23	chr15:79272400-79280200	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:79272400-79286400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:79272600-79280000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:79273600-79276400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr15:79274000-79276400	Enhancers	Adipose Nuclei	Adipose
28	chr15:79274000-79279400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:79274200-79276400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr15:79274400-79275800	Enhancers	HSMMtube	muscle
31	chr15:79274600-79276000	Enhancers	Fetal Muscle Leg	muscle
32	chr15:79274800-79276400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:79275000-79276400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:79275000-79276400	Enhancers	HepG2	liver
35	chr15:79275200-79276400	Enhancers	HSMM	muscle
36	chr15:79275200-79280000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:79275400-79275600	Enhancers	Spleen	Spleen
38	chr15:79275400-79276200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr15:79275400-79276200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr15:79275400-79276400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr15:79275400-79276400	ZNF genes & repeats	GM12878-XiMat	blood

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