Variant report

Variant	rs4290977
Chromosome Location	chr5:179515597-179515598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179497628..179501303-chr5:179515558..179519468,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10051632	0.85[ASN][1000 genomes]
rs13162328	0.87[ASN][1000 genomes]
rs13176402	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1540526	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1947056	0.95[ASN][1000 genomes]
rs2083966	0.95[ASN][1000 genomes]
rs3749821	0.87[ASN][1000 genomes]
rs4235506	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700858	0.87[ASN][1000 genomes]
rs4700862	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6601080	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723889	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7734867	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179499400-179517000	Weak transcription	Right Atrium	heart
2	chr5:179509400-179517200	Weak transcription	Liver	Liver
3	chr5:179510600-179517000	Weak transcription	Fetal Brain Female	brain
4	chr5:179512000-179516600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:179512600-179517000	Weak transcription	Placenta	Placenta
6	chr5:179512600-179517200	Weak transcription	Colonic Mucosa	Colon
7	chr5:179512800-179517000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:179512800-179517000	Weak transcription	Brain Germinal Matrix	brain
9	chr5:179512800-179517000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:179513000-179516800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:179513000-179516800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:179513000-179517000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:179513000-179517000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:179513000-179517000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:179513000-179517000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:179513000-179517000	Weak transcription	Fetal Intestine Large	intestine
17	chr5:179513000-179517200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:179513000-179517200	Weak transcription	Stomach Mucosa	stomach
19	chr5:179513200-179516000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:179513200-179517000	Weak transcription	Primary T cells from cord blood	blood
21	chr5:179513200-179517000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:179513200-179517000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr5:179513200-179517000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:179513200-179517000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:179513200-179517000	Weak transcription	Brain Angular Gyrus	brain
26	chr5:179513200-179517000	Weak transcription	Brain Anterior Caudate	brain
27	chr5:179513200-179517000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:179513200-179517000	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:179513200-179517000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:179513200-179517000	Weak transcription	Fetal Intestine Small	intestine
31	chr5:179513200-179517000	Weak transcription	Pancreas	Pancrea
32	chr5:179513200-179518000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:179513200-179520800	Weak transcription	Spleen	Spleen
34	chr5:179513800-179517000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:179514000-179516800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:179514000-179516800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:179514000-179517000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:179514200-179517000	Weak transcription	Fetal Thymus	thymus
39	chr5:179514400-179516800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr5:179514400-179517000	Weak transcription	K562	blood
41	chr5:179514800-179517000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:179515000-179516200	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr5:179515000-179516200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr5:179515000-179516400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr5:179515200-179515600	Bivalent Enhancer	Thymus	Thymus
46	chr5:179515200-179515800	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr5:179515200-179515800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:179515200-179516000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:179515200-179517000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr5:179515200-179517000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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