Variant report

Variant	rs2270824
Chromosome Location	chr5:80531585-80531586
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80530046..80533018-chr5:80537820..80540645,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248794	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10036376	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs10041063	0.81[CEU][hapmap]
rs10041138	0.84[CHB][hapmap]
rs10052929	0.85[CHB][hapmap]
rs10055018	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10071174	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10073527	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10514215	0.95[CEU][hapmap];0.84[YRI][hapmap]
rs10514216	0.89[EUR][1000 genomes]
rs11950033	0.81[CEU][hapmap]
rs11960275	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12516414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12652649	0.89[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12657721	0.90[JPT][hapmap]
rs12659947	0.80[JPT][hapmap]
rs13155580	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs13172928	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1566433	0.85[CHB][hapmap]
rs16876403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17294956	0.95[CEU][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes]
rs2270823	0.81[CEU][hapmap]
rs2277037	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291942	0.80[JPT][hapmap]
rs28819671	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2897390	0.81[CEU][hapmap]
rs4502795	0.89[CHB][hapmap]
rs4703828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4703832	0.86[AMR][1000 genomes]
rs4704709	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4704710	0.81[CEU][hapmap]
rs4704714	0.85[CHB][hapmap]
rs4704716	0.80[JPT][hapmap]
rs4704717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs545	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs57086010	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59563495	0.85[ASN][1000 genomes]
rs60434474	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6863732	0.85[CHB][hapmap]
rs6872183	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6893467	0.81[CEU][hapmap]
rs7448717	0.94[CEU][hapmap]
rs750728	0.95[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2270824	CTD-2248H3.1	cis	lung	GTEx
rs2270824	CTC-281B15.1	cis	lung	GTEx
rs2270824	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs2270824	CTC-281B15.1	cis	Thyroid	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
3	chr5:80528200-80531800	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr5:80528400-80531600	Enhancers	Spleen	Spleen
5	chr5:80528600-80531600	Enhancers	Fetal Thymus	thymus
6	chr5:80528600-80532000	Enhancers	Lung	lung
7	chr5:80529400-80531600	Weak transcription	Gastric	stomach
8	chr5:80529400-80531800	Weak transcription	Fetal Brain Female	brain
9	chr5:80529400-80532400	Weak transcription	Placenta	Placenta
10	chr5:80529400-80532400	Active TSS	Right Ventricle	heart
11	chr5:80529400-80535200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:80529400-80540800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:80529400-80541000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:80529400-80543400	Weak transcription	NHLF	lung
15	chr5:80529400-80544200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:80529600-80532000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr5:80529600-80532200	Enhancers	Adipose Nuclei	Adipose
19	chr5:80529600-80532400	Enhancers	Brain Anterior Caudate	brain
20	chr5:80529600-80535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:80529600-80541000	Weak transcription	Fetal Intestine Large	intestine
22	chr5:80529600-80542800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:80529800-80531800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr5:80529800-80531800	Enhancers	HSMMtube	muscle
26	chr5:80529800-80532200	Enhancers	Ovary	ovary
27	chr5:80529800-80532400	Enhancers	Brain Angular Gyrus	brain
28	chr5:80529800-80533000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
29	chr5:80530000-80531600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:80530000-80531600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:80530000-80531800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:80530000-80531800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:80530000-80532000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:80530000-80532400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr5:80530000-80532600	Flanking Active TSS	Fetal Heart	heart
36	chr5:80530000-80537200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:80530000-80546400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:80530200-80532200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:80530200-80532200	Enhancers	Dnd41	blood
40	chr5:80530200-80532400	Enhancers	Brain Hippocampus Middle	brain
41	chr5:80530200-80541600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:80530200-80544000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:80530400-80532000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr5:80530400-80532200	Genic enhancers	Fetal Muscle Leg	muscle
45	chr5:80530400-80532200	Flanking Active TSS	Right Atrium	heart
46	chr5:80530400-80532400	Enhancers	Brain Cingulate Gyrus	brain
47	chr5:80530400-80532400	Enhancers	Brain Substantia Nigra	brain
48	chr5:80530400-80532600	Strong transcription	Fetal Stomach	stomach
49	chr5:80530600-80532000	Enhancers	Fetal Muscle Trunk	muscle
50	chr5:80530600-80537400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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