Variant report

Variant	rs267300
Chromosome Location	chr5:114622705-114622706
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	chr5:114619634..114629040-chr5:114629951..114633566,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164221	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs117060	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs155414	0.91[CHB][hapmap]
rs166459	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs169088	0.92[CHB][hapmap]
rs185566	0.81[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2053697	0.85[CHB][hapmap];0.89[CHD][hapmap]
rs2112360	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2112361	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2124396	0.96[AMR][1000 genomes]
rs2545430	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs265412	1.00[ASW][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs265419	0.92[CHB][hapmap]
rs265420	0.92[CHB][hapmap]
rs265421	0.92[CHB][hapmap];0.92[CHD][hapmap]
rs265425	0.89[CHB][hapmap];0.92[CHD][hapmap]
rs265430	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs265435	0.83[CHB][hapmap]
rs265436	0.92[CHB][hapmap]
rs265439	0.92[CHB][hapmap]
rs265442	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs267286	1.00[ASW][hapmap];0.81[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs267287	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs267288	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs267290	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs267292	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs267295	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs267297	0.89[CHD][hapmap]
rs267298	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs267299	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267301	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs267302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs267303	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs267304	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs267306	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs267307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3100784	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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	nsv968978	chr5:114620599-114625007	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs267300	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114599000-114624000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:114599000-114626600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:114599000-114630800	Weak transcription	Psoas Muscle	Psoas
4	chr5:114599000-114631200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:114599000-114631200	Weak transcription	HSMM	muscle
6	chr5:114599000-114631400	Weak transcription	Left Ventricle	heart
7	chr5:114599200-114631200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:114601200-114631200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:114601200-114631400	Weak transcription	Aorta	Aorta
10	chr5:114604000-114630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:114611200-114630400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:114611200-114630400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:114611200-114630800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:114611400-114624200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr5:114611400-114627600	Weak transcription	Primary B cells from cord blood	blood
16	chr5:114611400-114628600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:114611600-114623200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:114612400-114625000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:114612800-114630200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:114620000-114622800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:114621400-114628600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:114621600-114628400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:114621600-114630400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:114622200-114625000	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:114622200-114625400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:114622400-114624200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr5:114622400-114630200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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