Variant report

Variant	rs28608482
Chromosome Location	chr4:7975579-7975580
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7938506..7945813-chr4:7968503..7977501,21	MCF-7	breast:
2	chr4:7943385..7945490-chr4:7973996..7976275,2	MCF-7	breast:
3	chr4:7974598..7977296-chr4:7995967..7999387,3	MCF-7	breast:
4	chr4:7940228..7942732-chr4:7972694..7975678,3	MCF-7	breast:
5	chr4:7973238..7976056-chr4:7980066..7981632,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11728588	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11734838	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55740839	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56249912	0.81[EUR][1000 genomes]
rs62290616	0.86[EUR][1000 genomes]
rs6447896	0.85[ASN][1000 genomes]
rs6812592	0.90[ASN][1000 genomes]
rs7662540	0.95[ASN][1000 genomes]
rs7699715	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv829851	chr4:7958698-8049060	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv878579	chr4:7969594-8011696	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7967000-7987600	Weak transcription	Psoas Muscle	Psoas
2	chr4:7969000-7975600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
3	chr4:7969200-7975600	Enhancers	Fetal Thymus	thymus
4	chr4:7969200-7975800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:7969400-7975800	Enhancers	Stomach Smooth Muscle	stomach
6	chr4:7969400-7976000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:7969600-7975800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr4:7970400-7980200	Weak transcription	HSMM	muscle
9	chr4:7970800-7975800	Enhancers	NH-A	brain
10	chr4:7971000-7976000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr4:7971000-7976000	Enhancers	HMEC	breast
12	chr4:7971200-7976000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:7971600-7975800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:7972200-7976200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:7972200-7979600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:7972200-7980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:7972400-7975600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:7972400-7975600	Enhancers	Esophagus	oesophagus
19	chr4:7972400-7975800	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:7972400-7976000	Enhancers	NHEK	skin
21	chr4:7972400-7978400	Weak transcription	Fetal Kidney	kidney
22	chr4:7972400-7980200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:7972600-7976000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:7972600-7976000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:7972800-7975600	Enhancers	Fetal Intestine Large	intestine
26	chr4:7972800-7975600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr4:7973000-7975600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr4:7973000-7975600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:7973000-7975600	Enhancers	Stomach Mucosa	stomach
30	chr4:7973000-7976000	Enhancers	Placenta	Placenta
31	chr4:7973000-7978400	Weak transcription	Fetal Lung	lung
32	chr4:7973000-7980000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:7973000-7980200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:7973000-7980200	Weak transcription	Adipose Nuclei	Adipose
35	chr4:7973200-7975600	Enhancers	A549	lung
36	chr4:7973200-7975600	Enhancers	GM12878-XiMat	blood
37	chr4:7973400-7978400	Weak transcription	Fetal Brain Male	brain
38	chr4:7973400-7978400	Weak transcription	Fetal Heart	heart
39	chr4:7973600-7975600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr4:7973600-7975800	Enhancers	NHLF	lung
41	chr4:7973600-7976000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:7973600-7976800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:7973600-7980400	Weak transcription	Ovary	ovary
44	chr4:7973800-7975600	Enhancers	Brain Angular Gyrus	brain
45	chr4:7973800-7975800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr4:7974000-7975800	Genic enhancers	Fetal Intestine Small	intestine
47	chr4:7974200-7976000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:7974200-7976000	Enhancers	Osteobl	bone
49	chr4:7974400-7975800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:7974400-7975800	Enhancers	Brain Hippocampus Middle	brain

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