Variant report

Variant	rs28778886
Chromosome Location	chr4:15604956-15604957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10018878	1.00[AMR][1000 genomes]
rs16891806	1.00[AMR][1000 genomes]
rs16891831	1.00[AMR][1000 genomes]
rs28402830	1.00[AMR][1000 genomes]
rs28493206	1.00[AMR][1000 genomes]
rs28578650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28583158	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28712663	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6841413	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998617	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
2	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
3	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
4	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
5	chr4:15565600-15611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:15565800-15605000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:15568400-15655600	Weak transcription	Gastric	stomach
8	chr4:15575200-15618000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:15587200-15612600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:15589800-15621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:15590000-15615600	Weak transcription	Lung	lung
12	chr4:15590600-15626400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:15593800-15621200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:15594000-15607200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:15594000-15609200	Weak transcription	Psoas Muscle	Psoas
16	chr4:15594600-15617800	Weak transcription	Right Ventricle	heart
17	chr4:15595000-15605200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:15595000-15606000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:15595400-15605400	Weak transcription	Fetal Brain Male	brain
20	chr4:15595400-15614000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:15595800-15611400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:15596000-15608000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:15596000-15612800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:15596400-15606600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:15596600-15616400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:15596800-15610000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:15597200-15620600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr4:15598400-15605000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:15598400-15608800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:15598600-15607400	Strong transcription	NHDF-Ad	bronchial
31	chr4:15598600-15607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:15598600-15611200	Strong transcription	HSMM	muscle
33	chr4:15599200-15605000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:15599200-15605000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr4:15599200-15607400	Strong transcription	Fetal Lung	lung
36	chr4:15599400-15605000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:15599600-15606800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:15599600-15610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:15600400-15605200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:15600400-15606800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:15600600-15605800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr4:15600600-15620800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr4:15600800-15653000	Weak transcription	Colonic Mucosa	Colon
44	chr4:15601000-15606400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr4:15601000-15651600	Weak transcription	Small Intestine	intestine
46	chr4:15601200-15607200	Strong transcription	Primary B cells from cord blood	blood
47	chr4:15601400-15606000	Weak transcription	Fetal Heart	heart
48	chr4:15601600-15605000	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:15601600-15607600	Strong transcription	Osteobl	bone
50	chr4:15601800-15606400	Strong transcription	Brain Hippocampus Middle	brain

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