Variant report

Variant	rs2303080
Chromosome Location	chr5:7878424-7878425
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7875376..7880031-chr5:7885320..7890237,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16879334	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16879342	0.96[EUR][1000 genomes]
rs16879455	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277957	0.96[EUR][1000 genomes]
rs2287779	0.96[EUR][1000 genomes]
rs2287780	0.96[EUR][1000 genomes]
rs2303082	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756439	0.96[EUR][1000 genomes]
rs3776458	0.96[EUR][1000 genomes]
rs3776460	0.96[EUR][1000 genomes]
rs3776463	0.96[EUR][1000 genomes]
rs3776464	0.89[EUR][1000 genomes]
rs3816908	0.96[EUR][1000 genomes]
rs3822442	0.96[EUR][1000 genomes]
rs3822443	0.96[EUR][1000 genomes]
rs59809395	0.96[EUR][1000 genomes]
rs60817278	0.96[EUR][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	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 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	chr5:7870200-7879800	Weak transcription	Pancreas	Pancrea
2	chr5:7870200-7882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:7870800-7879800	Weak transcription	Colonic Mucosa	Colon
5	chr5:7871000-7894000	Weak transcription	Fetal Heart	heart
6	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:7871400-7902400	Strong transcription	K562	blood
10	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:7871600-7886800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:7871600-7887200	Strong transcription	Fetal Thymus	thymus
13	chr5:7871600-7887600	Strong transcription	Placenta	Placenta
14	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:7871800-7884800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:7872000-7886400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:7872000-7895200	Strong transcription	Fetal Muscle Leg	muscle
22	chr5:7872800-7887400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:7873000-7882200	Strong transcription	Fetal Lung	lung
24	chr5:7873200-7887600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:7873200-7903400	Strong transcription	Dnd41	blood
26	chr5:7873400-7878800	Strong transcription	Lung	lung
27	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
28	chr5:7874000-7879200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:7874000-7879200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr5:7874000-7890800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
32	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:7874200-7887000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr5:7874600-7894400	Strong transcription	Adipose Nuclei	Adipose
35	chr5:7874800-7879000	Strong transcription	Fetal Kidney	kidney
36	chr5:7874800-7881400	Strong transcription	Brain Germinal Matrix	brain
37	chr5:7874800-7887400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:7874800-7887600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:7875200-7881800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr5:7875400-7878600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:7875400-7879400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:7875400-7879400	Strong transcription	HUVEC	blood vessel
44	chr5:7875400-7884200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr5:7875400-7884600	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr5:7875400-7886200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:7875400-7887200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:7875400-7887400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:7875400-7895200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr5:7875400-7903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links