Variant report

Variant	rs72840147
Chromosome Location	chr17:20978155-20978156
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	chr17:20945081..20946975-chr17:20977451..20979833,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11867665	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11871072	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12600703	0.83[ASN][1000 genomes]
rs28502198	0.91[ASN][1000 genomes]
rs4985975	0.84[ASN][1000 genomes]
rs872789	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9797242	0.80[ASN][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	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs72840147	RP11-344E13.3	cis	Stomach	GTEx
rs72840147	RP11-344E13.3	cis	Whole Blood	GTEx
rs72840147	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs72840147	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs72840147	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs72840147	RP11-344E13.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20970200-20978600	Weak transcription	HSMMtube	muscle
2	chr17:20974200-20978400	Weak transcription	HSMM	muscle
3	chr17:20975000-20983400	Enhancers	Fetal Brain Male	brain
4	chr17:20975400-20979000	Enhancers	Fetal Muscle Trunk	muscle
5	chr17:20976200-20979000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:20976200-20989000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:20976400-20978800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:20976600-20978400	Weak transcription	Brain Hippocampus Middle	brain
9	chr17:20976800-20978400	Weak transcription	Fetal Stomach	stomach
10	chr17:20977000-20978200	Weak transcription	Fetal Muscle Leg	muscle
11	chr17:20977400-20978200	Enhancers	Brain Germinal Matrix	brain
12	chr17:20977400-20978400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr17:20977600-20978600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:20977600-20978800	Weak transcription	Fetal Brain Female	brain
15	chr17:20977600-20979000	Enhancers	Rectal Smooth Muscle	rectum
16	chr17:20977800-20978200	Enhancers	Stomach Smooth Muscle	stomach
17	chr17:20977800-20979000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr17:20978000-20978400	Weak transcription	NH-A	brain
19	chr17:20978000-20978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:20978000-20978600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:20978000-20981400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:20978000-20983200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links