Variant report

Variant	rs1238951
Chromosome Location	chr5:79915790-79915791
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	chr5:79910821..79913397-chr5:79915125..79917648,2	MCF-7	breast:
2	chr5:79914495..79916896-chr5:79948038..79951865,3	K562	blood:

Variant related genes	Relation type
ENSG00000113318	Chromatin interaction
ENSG00000228716	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1643656	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1650660	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1650684	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1650687	0.82[EUR][1000 genomes]
rs1650716	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1650723	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1677658	0.82[EUR][1000 genomes]
rs1677697	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1677705	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6151616	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151636	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs836789	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs836790	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs836791	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs836792	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs836803	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1238951	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs1238951	MSH3	cis	Thyroid	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79902400-79916600	Weak transcription	Thymus	Thymus
2	chr5:79904800-79925000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:79906600-79949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:79909400-79916200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:79909800-79927200	Weak transcription	Primary T cells from cord blood	blood
6	chr5:79910600-79927000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:79911600-79925400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:79911600-79925400	Weak transcription	Adipose Nuclei	Adipose
9	chr5:79911800-79915800	Weak transcription	NH-A	brain
10	chr5:79911800-79916200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:79911800-79916200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:79911800-79925200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:79911800-79927200	Weak transcription	HMEC	breast
14	chr5:79912000-79926400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:79912000-79926600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:79912000-79938000	Weak transcription	Brain Anterior Caudate	brain
17	chr5:79912200-79928600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:79912200-79948000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr5:79912400-79925000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:79912800-79925200	Weak transcription	Fetal Thymus	thymus
21	chr5:79913200-79925200	Weak transcription	Hela-S3	cervix
22	chr5:79913200-79949000	Weak transcription	Spleen	Spleen
23	chr5:79913400-79921400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:79913400-79926800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:79913600-79925000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:79913600-79949400	Weak transcription	Esophagus	oesophagus
27	chr5:79913800-79927200	Weak transcription	A549	lung
28	chr5:79914200-79949400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:79914400-79916800	Strong transcription	Dnd41	blood
30	chr5:79914600-79925600	Weak transcription	Fetal Stomach	stomach
31	chr5:79914800-79916200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr5:79914800-79916400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:79914800-79927400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:79915000-79916200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:79915400-79919400	Weak transcription	Fetal Intestine Small	intestine
36	chr5:79915400-79925000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:79915400-79925600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:79915400-79949200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:79915600-79919400	Weak transcription	Fetal Intestine Large	intestine
40	chr5:79915600-79934600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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