Variant report

Variant	rs28655476
Chromosome Location	chr4:7893561-7893562
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	chr4:7891241..7895444-chr4:7905345..7908483,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs13137140	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17770147	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17770177	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28394221	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28432831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492032	0.91[AFR][1000 genomes]
rs28539821	0.82[EUR][1000 genomes]
rs28547902	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28605531	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28673208	0.82[EUR][1000 genomes]
rs28688265	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28733584	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28754920	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34075381	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34092549	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34119140	0.81[EUR][1000 genomes]
rs34121576	0.81[EUR][1000 genomes]
rs34181918	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34189407	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34221000	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34392913	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34570748	0.81[EUR][1000 genomes]
rs34652148	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34712341	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34868842	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34869495	0.80[AFR][1000 genomes]
rs35114566	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs35152796	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35154266	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35238070	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35502845	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35727635	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35735994	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35933973	0.81[EUR][1000 genomes]
rs35967175	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs36013696	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36046241	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs36106793	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4296663	0.91[AFR][1000 genomes]
rs4411970	0.91[AFR][1000 genomes]
rs6824266	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6829505	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6838055	0.91[AFR][1000 genomes]
rs6845014	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs71600561	0.80[EUR][1000 genomes]
rs71601888	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs71601889	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs71601890	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs71601892	0.91[AFR][1000 genomes];0.81[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	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	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:7881800-7896600	Weak transcription	Lung	lung
6	chr4:7883200-7904400	Weak transcription	Gastric	stomach
7	chr4:7886000-7895800	Weak transcription	Esophagus	oesophagus
8	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
9	chr4:7889200-7901200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:7890800-7893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:7891400-7894000	Weak transcription	Fetal Intestine Small	intestine
12	chr4:7891600-7894800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:7891600-7894800	Enhancers	Colon Smooth Muscle	Colon
14	chr4:7891600-7895000	Enhancers	NHDF-Ad	bronchial
15	chr4:7891800-7893600	Enhancers	HSMMtube	muscle
16	chr4:7891800-7893800	Enhancers	Stomach Smooth Muscle	stomach
17	chr4:7891800-7894000	Enhancers	Hela-S3	cervix
18	chr4:7891800-7894400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:7891800-7894400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr4:7891800-7894400	Enhancers	Rectal Smooth Muscle	rectum
21	chr4:7891800-7894400	Enhancers	HepG2	liver
22	chr4:7891800-7894400	Enhancers	NHEK	skin
23	chr4:7891800-7894800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:7891800-7894800	Enhancers	Fetal Heart	heart
25	chr4:7891800-7894800	Enhancers	HMEC	breast
26	chr4:7891800-7895000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr4:7891800-7895400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:7891800-7895800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:7892000-7893600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr4:7892000-7894400	Enhancers	Brain Substantia Nigra	brain
31	chr4:7892000-7894600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr4:7892000-7894600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr4:7892000-7897000	Enhancers	Brain Germinal Matrix	brain
34	chr4:7892400-7893600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:7892400-7893600	Enhancers	Adipose Nuclei	Adipose
36	chr4:7892400-7894200	Enhancers	Brain Hippocampus Middle	brain
37	chr4:7892400-7894400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr4:7892400-7894600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:7892400-7894600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr4:7892400-7894600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr4:7892400-7894800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:7892400-7897000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr4:7892600-7894600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:7892600-7894600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr4:7892600-7894600	Enhancers	Fetal Muscle Leg	muscle
46	chr4:7892600-7894800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:7892600-7903800	Weak transcription	Stomach Mucosa	stomach
48	chr4:7892800-7894000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:7892800-7894000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:7892800-7894400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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