Variant report

Variant	rs9962328
Chromosome Location	chr18:13230447-13230448
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	chr18:13229701..13231556-chr18:13232508..13235407,3	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12458598	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12955200	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12968182	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12968748	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3901403	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4277409	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4616353	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4797744	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4797747	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4797749	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4797750	0.90[EUR][1000 genomes]
rs6505789	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67772629	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7228009	0.84[EUR][1000 genomes]
rs7244519	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9944928	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9952107	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9952186	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9952516	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9952649	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9955376	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9955747	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9958724	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9967502	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv909409	chr18:13151544-13240284	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv909410	chr18:13151544-13308950	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13223000-13231000	Genic enhancers	Fetal Thymus	thymus
2	chr18:13223400-13232600	Weak transcription	Fetal Intestine Large	intestine
3	chr18:13223400-13235400	Weak transcription	Fetal Kidney	kidney
4	chr18:13223600-13232200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr18:13223600-13235600	Weak transcription	Fetal Intestine Small	intestine
6	chr18:13223600-13241400	Weak transcription	Aorta	Aorta
7	chr18:13223800-13232400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:13223800-13234200	Weak transcription	Liver	Liver
9	chr18:13223800-13259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr18:13224000-13232000	Weak transcription	Gastric	stomach
11	chr18:13224000-13234800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr18:13224000-13235400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr18:13224000-13259800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr18:13224200-13232000	Weak transcription	Brain Angular Gyrus	brain
15	chr18:13224200-13233400	Weak transcription	HepG2	liver
16	chr18:13224400-13231200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr18:13224400-13231200	Weak transcription	Fetal Muscle Leg	muscle
18	chr18:13224400-13231600	Weak transcription	Brain Hippocampus Middle	brain
19	chr18:13224400-13232000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr18:13224400-13232000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr18:13224400-13232000	Weak transcription	Brain Substantia Nigra	brain
22	chr18:13224400-13232200	Weak transcription	Adipose Nuclei	Adipose
23	chr18:13224400-13232200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr18:13224400-13232400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:13224400-13234000	Weak transcription	Pancreas	Pancrea
26	chr18:13224400-13234600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr18:13224400-13235400	Weak transcription	Colon Smooth Muscle	Colon
28	chr18:13224400-13235600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr18:13224400-13242600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr18:13224400-13245400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr18:13224400-13259800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr18:13224600-13232000	Weak transcription	Brain Anterior Caudate	brain
33	chr18:13225000-13231200	Weak transcription	Fetal Lung	lung
34	chr18:13225400-13232000	Weak transcription	Right Atrium	heart
35	chr18:13225600-13232600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr18:13227000-13231000	Strong transcription	Fetal Stomach	stomach
37	chr18:13228200-13232800	Weak transcription	Esophagus	oesophagus
38	chr18:13228400-13232200	Weak transcription	Spleen	Spleen
39	chr18:13229400-13232000	Weak transcription	Psoas Muscle	Psoas
40	chr18:13229400-13243000	Weak transcription	Dnd41	blood
41	chr18:13229800-13231200	Weak transcription	Brain Germinal Matrix	brain
42	chr18:13229800-13233000	Weak transcription	Primary T cells from cord blood	blood
43	chr18:13230000-13231200	Weak transcription	Left Ventricle	heart
44	chr18:13230000-13231200	Weak transcription	Right Ventricle	heart
45	chr18:13230000-13231400	Strong transcription	Fetal Brain Female	brain
46	chr18:13230000-13231600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr18:13230200-13230600	Weak transcription	Fetal Brain Male	brain
48	chr18:13230200-13231400	Weak transcription	Fetal Heart	heart
49	chr18:13230200-13232000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr18:13230400-13232600	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links