Variant report

Variant	rs872789
Chromosome Location	chr17:20979206-20979207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20945081..20946975-chr17:20977451..20979833,2	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-2	chr17:20978881-20979270	XLOC_012142
2	lnc-DHRS7B-2	chr17:20978881-20979270	XLOC_012142
3	lnc-DHRS7B-2	chr17:20978869-20979270	XLOC_012142
4	lnc-DHRS7B-2	chr17:20978881-20979270	XLOC_012142
5	lnc-DHRS7B-2	chr17:20978868-20980034	NONHSAT052157

No data

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11867665	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11871072	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12600703	0.82[ASN][1000 genomes]
rs28502198	0.89[ASN][1000 genomes]
rs4985975	0.83[ASN][1000 genomes]
rs72840147	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs872789	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs872789	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs872789	RP11-344E13.3	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20975000-20983400	Enhancers	Fetal Brain Male	brain
2	chr17:20976200-20989000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:20978000-20981400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:20978000-20983200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:20978400-20979400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:20978400-20979400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:20978400-20979400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:20978400-20979400	Active TSS	Brain Angular Gyrus	brain
9	chr17:20978400-20979400	Enhancers	Fetal Stomach	stomach
10	chr17:20978400-20979600	Active TSS	Brain Hippocampus Middle	brain
11	chr17:20978400-20979600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:20978400-20979600	Enhancers	NH-A	brain
13	chr17:20978400-20980000	Active TSS	Brain Anterior Caudate	brain
14	chr17:20978400-20980000	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr17:20978600-20979400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:20978600-20979400	Enhancers	HMEC	breast
17	chr17:20978600-20979400	Enhancers	NHEK	skin
18	chr17:20978600-20979800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:20978600-20980600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr17:20978600-20981200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:20978800-20979400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr17:20978800-20979400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr17:20978800-20979800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:20978800-20979800	Active TSS	Brain Cingulate Gyrus	brain
25	chr17:20979000-20979400	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr17:20979000-20979400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr17:20979000-20979400	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr17:20979000-20979400	Enhancers	Placenta	Placenta
29	chr17:20979000-20979600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr17:20979000-20979600	Flanking Active TSS	Rectal Smooth Muscle	rectum
31	chr17:20979000-20979800	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr17:20979000-20979800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr17:20979000-20980400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr17:20979000-20980400	Flanking Active TSS	HSMM	muscle
35	chr17:20979000-20981400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:20979200-20979400	Active TSS	Brain Germinal Matrix	brain
37	chr17:20979200-20979400	Active TSS	Fetal Brain Female	brain
38	chr17:20979200-20979400	Enhancers	NHDF-Ad	bronchial
39	chr17:20979200-20979600	Active TSS	Brain Substantia Nigra	brain
40	chr17:20979200-20979800	Flanking Active TSS	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links