Variant report

Variant	rs9952107
Chromosome Location	chr18:13234323-13234324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:13229701..13231556-chr18:13232508..13235407,3	MCF-7	breast:
2	chr18:13226398..13229560-chr18:13232125..13236070,6	MCF-7	breast:
3	chr18:13216483..13218902-chr18:13232674..13234716,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168675	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12458598	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12607576	0.89[CHD][hapmap];0.81[GIH][hapmap]
rs12955200	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12968182	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12968748	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3901403	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4277409	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4616353	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4797744	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4797747	0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4797749	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4797750	0.89[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs4797752	0.84[MEX][hapmap]
rs6505789	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67772629	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7228009	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7244519	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9944928	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9952186	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9952516	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9952649	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9955376	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9955747	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9958724	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9962328	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9967502	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13223400-13235400	Weak transcription	Fetal Kidney	kidney
2	chr18:13223600-13235600	Weak transcription	Fetal Intestine Small	intestine
3	chr18:13223600-13241400	Weak transcription	Aorta	Aorta
4	chr18:13223800-13259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr18:13224000-13234800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr18:13224000-13235400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr18:13224000-13259800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr18:13224400-13234600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr18:13224400-13235400	Weak transcription	Colon Smooth Muscle	Colon
10	chr18:13224400-13235600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr18:13224400-13242600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr18:13224400-13245400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr18:13224400-13259800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr18:13229400-13243000	Weak transcription	Dnd41	blood
15	chr18:13230600-13240800	Enhancers	Fetal Brain Male	brain
16	chr18:13231800-13234600	Enhancers	Left Ventricle	heart
17	chr18:13231800-13234800	Enhancers	Right Ventricle	heart
18	chr18:13232000-13234800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr18:13232800-13246200	Weak transcription	Psoas Muscle	Psoas
20	chr18:13233000-13235000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr18:13233000-13235400	Weak transcription	Adipose Nuclei	Adipose
22	chr18:13233000-13236200	Enhancers	Brain Substantia Nigra	brain
23	chr18:13233000-13239600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr18:13233000-13241400	Enhancers	Fetal Brain Female	brain
25	chr18:13233000-13260200	Weak transcription	Colonic Mucosa	Colon
26	chr18:13233200-13234800	Strong transcription	Thymus	Thymus
27	chr18:13233200-13240600	Enhancers	Brain Anterior Caudate	brain
28	chr18:13233200-13245800	Weak transcription	Right Atrium	heart
29	chr18:13233400-13235400	Weak transcription	Brain Germinal Matrix	brain
30	chr18:13233400-13235600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr18:13233400-13239600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr18:13233400-13254000	Weak transcription	Spleen	Spleen
33	chr18:13233400-13259000	Weak transcription	Primary T cells from cord blood	blood
34	chr18:13233600-13235400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr18:13233600-13235600	Weak transcription	Brain Hippocampus Middle	brain
36	chr18:13233600-13235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr18:13233600-13235600	Weak transcription	Fetal Lung	lung
38	chr18:13233600-13243000	Weak transcription	Gastric	stomach
39	chr18:13233800-13234800	Flanking Active TSS	HepG2	liver
40	chr18:13233800-13235600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr18:13234000-13234400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr18:13234000-13234800	Enhancers	Pancreas	Pancrea
43	chr18:13234000-13235000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr18:13234000-13235600	Weak transcription	Fetal Thymus	thymus
45	chr18:13234200-13234400	Enhancers	Brain Angular Gyrus	brain
46	chr18:13234200-13234600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr18:13234200-13234800	Enhancers	Liver	Liver
48	chr18:13234200-13234800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr18:13234200-13235200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr18:13234200-13235600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links