Variant report

Variant	rs9916917
Chromosome Location	chr18:29871293-29871294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr18:29871227-29871384	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29868718..29871349-chr18:30049265..30052223,3	MCF-7	breast:

Variant related genes	Relation type
GAREM	TF binding region
ENSG00000141441	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11660076	0.93[EUR][1000 genomes]
rs11661174	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11661186	0.86[EUR][1000 genomes]
rs11665544	0.93[EUR][1000 genomes]
rs16962918	0.89[EUR][1000 genomes]
rs16962924	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16962941	0.93[EUR][1000 genomes]
rs16962953	0.89[EUR][1000 genomes]
rs16962965	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16962971	0.93[EUR][1000 genomes]
rs16962974	0.93[EUR][1000 genomes]
rs16962977	0.93[EUR][1000 genomes]
rs28482447	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28540269	0.89[AFR][1000 genomes]
rs28673618	0.89[AFR][1000 genomes]
rs3859366	0.89[EUR][1000 genomes]
rs4462681	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60291556	0.89[EUR][1000 genomes]
rs7243861	0.86[EUR][1000 genomes]
rs7243963	0.86[EUR][1000 genomes]
rs73419859	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs8086611	0.93[EUR][1000 genomes]
rs8086990	0.93[EUR][1000 genomes]
rs8087394	0.89[EUR][1000 genomes]
rs9947150	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9950965	0.83[EUR][1000 genomes]
rs9953127	0.93[EUR][1000 genomes]
rs9960751	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9962307	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv528846	chr18:29832147-29890042	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29839800-29871800	Weak transcription	HSMMtube	muscle
2	chr18:29850000-29877600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr18:29858600-29877600	Weak transcription	Fetal Kidney	kidney
4	chr18:29861000-29876000	Weak transcription	Small Intestine	intestine
5	chr18:29861600-29876800	Weak transcription	Stomach Mucosa	stomach
6	chr18:29862400-29872400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr18:29863200-29873000	Weak transcription	Right Ventricle	heart
8	chr18:29863200-29877000	Weak transcription	Fetal Heart	heart
9	chr18:29864400-29880800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr18:29864600-29881200	Weak transcription	Colon Smooth Muscle	Colon
11	chr18:29865600-29873200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr18:29867800-29872400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:29867800-29873200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr18:29867800-29877800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr18:29867800-29878000	Weak transcription	Fetal Lung	lung
16	chr18:29867800-29880400	Weak transcription	Aorta	Aorta
17	chr18:29867800-29881800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr18:29868000-29871600	Weak transcription	Liver	Liver
19	chr18:29868000-29871800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr18:29868000-29872400	Weak transcription	Pancreas	Pancrea
21	chr18:29868000-29872800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr18:29868000-29873000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr18:29868000-29876200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr18:29868000-29877600	Weak transcription	Fetal Brain Female	brain
25	chr18:29868000-29877800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr18:29868000-29878000	Weak transcription	Adipose Nuclei	Adipose
27	chr18:29868000-29878200	Weak transcription	Brain Angular Gyrus	brain
28	chr18:29868000-29878200	Weak transcription	Fetal Stomach	stomach
29	chr18:29868000-29888800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:29868000-29888800	Weak transcription	Brain Hippocampus Middle	brain
31	chr18:29868000-29889000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr18:29868000-29889000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr18:29868200-29871600	Weak transcription	Fetal Muscle Leg	muscle
34	chr18:29868200-29873200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr18:29868200-29889800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr18:29868200-29923800	Weak transcription	Gastric	stomach
37	chr18:29870000-29878000	Weak transcription	Brain Anterior Caudate	brain
38	chr18:29871000-29876800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links