Variant report

Variant	rs55638925
Chromosome Location	chr5:179006870-179006871
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	chr5:179004969..179007855-chr5:179049122..179050815,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs56030209	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56252946	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56383177	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57104438	1.00[AMR][1000 genomes]
rs57418901	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61371983	1.00[AMR][1000 genomes]
rs6883330	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809473	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809478	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809479	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809480	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809481	1.00[AMR][1000 genomes]
rs73809482	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809486	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809487	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809489	1.00[AMR][1000 genomes]
rs73809490	1.00[AMR][1000 genomes]
rs73809491	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809492	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809493	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73809494	1.00[AMR][1000 genomes]
rs73809495	1.00[AMR][1000 genomes]
rs73809496	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73810811	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73810812	0.82[AFR][1000 genomes]
rs7704400	1.00[AMR][1000 genomes]
rs7704860	1.00[AMR][1000 genomes]
rs7704894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7705702	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
5	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
6	nsv883269	chr5:178951106-179031595	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
8	nsv1015477	chr5:178954409-179016804	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv883271	chr5:178955046-179031595	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv883272	chr5:178961872-179031595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1028236	chr5:178962087-179019981	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178987200-179040800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:178987400-179013200	Strong transcription	Fetal Stomach	stomach
3	chr5:178987400-179019800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:178987600-179045600	Strong transcription	Fetal Intestine Small	intestine
5	chr5:178987800-179009600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr5:178987800-179012200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:178987800-179017000	Strong transcription	Osteobl	bone
8	chr5:178987800-179031000	Strong transcription	Fetal Muscle Leg	muscle
9	chr5:178987800-179045600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:178988000-179009600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:178988400-179010200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:178989000-179010200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:178991200-179016600	Weak transcription	Stomach Mucosa	stomach
14	chr5:178996200-179022600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:178996600-179013200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:178996800-179034000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:178997600-179012800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:178997600-179020200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:178998400-179007600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:178998400-179012800	Weak transcription	HSMM	muscle
21	chr5:178999400-179012800	Weak transcription	HMEC	breast
22	chr5:178999800-179007600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr5:178999800-179007600	Weak transcription	Right Ventricle	heart
24	chr5:178999800-179013000	Weak transcription	Brain Substantia Nigra	brain
25	chr5:178999800-179013800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr5:178999800-179034800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:179000000-179008200	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:179000000-179013000	Weak transcription	Psoas Muscle	Psoas
29	chr5:179000000-179034200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:179000400-179022800	Weak transcription	Fetal Heart	heart
31	chr5:179001400-179008200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:179002000-179009600	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr5:179002200-179008600	Strong transcription	NH-A	brain
34	chr5:179002200-179009800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:179002200-179010000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:179002200-179017000	Strong transcription	Brain Germinal Matrix	brain
37	chr5:179002200-179022800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:179002200-179045600	Strong transcription	Fetal Intestine Large	intestine
39	chr5:179002600-179008200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:179002600-179013200	Weak transcription	K562	blood
41	chr5:179002800-179007600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr5:179002800-179007600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:179002800-179007600	Weak transcription	HepG2	liver
44	chr5:179002800-179008000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:179002800-179008200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr5:179002800-179012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:179002800-179012600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:179002800-179012800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:179002800-179012800	Weak transcription	GM12878-XiMat	blood
50	chr5:179003000-179007600	Weak transcription	Aorta	Aorta

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