Variant report

Variant	rs5997363
Chromosome Location	chr22:28794069-28794070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28789180..28790711-chr22:28793203..28795069,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12157518	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs16986103	0.81[ASN][1000 genomes]
rs16986290	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs16986377	0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16986462	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16986548	0.86[ASN][1000 genomes]
rs35731009	0.86[ASN][1000 genomes]
rs5762534	0.82[YRI][hapmap]
rs58427200	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997341	0.81[ASN][1000 genomes]
rs5997355	0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs5997365	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs5997367	1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs5997369	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997372	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005726	0.81[ASN][1000 genomes]
rs6005733	0.86[ASN][1000 genomes]
rs6005735	0.86[ASN][1000 genomes]
rs6005751	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6005757	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6005758	0.90[ASN][1000 genomes]
rs6005765	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6005779	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005780	0.86[EUR][1000 genomes]
rs6005783	0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs6005789	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005793	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005829	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6005833	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6005834	0.81[ASN][1000 genomes]
rs73427747	0.86[ASN][1000 genomes]
rs73428082	0.95[ASN][1000 genomes]
rs73428096	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73430108	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7510988	0.86[ASN][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28789800-28794600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr22:28789800-28794600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr22:28789800-28796200	Enhancers	Fetal Lung	lung
4	chr22:28790400-28794600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr22:28790400-28795400	Enhancers	Brain Substantia Nigra	brain
6	chr22:28790600-28794200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr22:28790600-28794200	Enhancers	NHDF-Ad	bronchial
8	chr22:28790600-28795600	Enhancers	Ovary	ovary
9	chr22:28791400-28800400	Weak transcription	Fetal Muscle Leg	muscle
10	chr22:28791600-28795400	Weak transcription	Lung	lung
11	chr22:28791600-28797600	Weak transcription	Placenta	Placenta
12	chr22:28791800-28795200	Enhancers	Adipose Nuclei	Adipose
13	chr22:28791800-28795200	Enhancers	Dnd41	blood
14	chr22:28792000-28794600	Enhancers	Fetal Stomach	stomach
15	chr22:28792000-28795000	Enhancers	Brain Anterior Caudate	brain
16	chr22:28792000-28795200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr22:28792000-28795400	Enhancers	Brain Hippocampus Middle	brain
18	chr22:28792000-28795600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr22:28792200-28794200	Enhancers	Fetal Heart	heart
20	chr22:28792200-28794800	Enhancers	Brain Angular Gyrus	brain
21	chr22:28792200-28795200	Enhancers	Brain Cingulate Gyrus	brain
22	chr22:28792400-28795400	Enhancers	Fetal Brain Male	brain
23	chr22:28792600-28801800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:28792800-28795400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr22:28792800-28795400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr22:28792800-28805200	Weak transcription	Fetal Intestine Large	intestine
27	chr22:28793000-28794200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr22:28793000-28794400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr22:28793000-28798000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr22:28793000-28808200	Weak transcription	Aorta	Aorta
31	chr22:28793000-28808600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr22:28793000-28814000	Weak transcription	Left Ventricle	heart
33	chr22:28793000-28819800	Weak transcription	Fetal Intestine Small	intestine
34	chr22:28793200-28794800	Weak transcription	Osteobl	bone
35	chr22:28793200-28795000	Enhancers	Fetal Brain Female	brain
36	chr22:28793400-28794400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr22:28793400-28795000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr22:28793400-28797400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr22:28793400-28806200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr22:28793600-28794200	Enhancers	Psoas Muscle	Psoas
41	chr22:28793800-28795000	Weak transcription	NHLF	lung
42	chr22:28794000-28794200	Enhancers	Liver	Liver
43	chr22:28794000-28794200	Enhancers	Right Ventricle	heart
44	chr22:28794000-28794600	Enhancers	Gastric	stomach
45	chr22:28794000-28795000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links