Variant report

Variant	rs11955202
Chromosome Location	chr5:124392359-124392360
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:124385684..124387313-chr5:124391971..124393955,2	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]
rs10040754	0.83[ASN][1000 genomes]
rs11241784	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28649435	0.91[ASN][1000 genomes]
rs4075487	0.91[ASN][1000 genomes]
rs4293913	0.85[ASN][1000 genomes]
rs4451044	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4510579	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4555796	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4836144	0.89[ASN][1000 genomes]
rs55888913	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55919034	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58908150	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59612060	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62372843	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62372851	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6595573	0.85[ASN][1000 genomes]
rs6866873	0.91[ASN][1000 genomes]
rs6872841	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72787446	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7444307	0.96[ASN][1000 genomes]
rs7446011	0.91[ASN][1000 genomes]
rs7700716	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7711673	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9686683	0.91[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	nsv882822	chr5:124250018-124449375	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830474	chr5:124263628-124431299	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv4984	chr5:124377028-124401500	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv830475	chr5:124387292-124550256	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124382800-124394200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:124382800-124394200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:124387200-124392400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:124387200-124392400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:124387200-124392400	Weak transcription	Brain Substantia Nigra	brain
6	chr5:124387400-124392400	Weak transcription	Aorta	Aorta
7	chr5:124388400-124396400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:124388400-124396400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:124388600-124392400	Weak transcription	Left Ventricle	heart
10	chr5:124388600-124395000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:124389600-124396200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr5:124390200-124392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:124390200-124392400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:124390200-124392400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:124390400-124392600	Weak transcription	Right Atrium	heart
16	chr5:124390600-124396400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:124390800-124395400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:124391000-124393200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr5:124391200-124396000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr5:124391600-124392800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr5:124391600-124396000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr5:124391600-124396200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:124391600-124398000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr5:124391800-124393000	Enhancers	Dnd41	blood
25	chr5:124391800-124396400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:124392000-124392800	Enhancers	Primary B cells from cord blood	blood
27	chr5:124392000-124392800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr5:124392000-124392800	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr5:124392000-124395800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr5:124392200-124392600	Enhancers	Brain Anterior Caudate	brain
31	chr5:124392200-124392600	Enhancers	Colon Smooth Muscle	Colon
32	chr5:124392200-124392600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr5:124392200-124392600	Enhancers	NHEK	skin
34	chr5:124392200-124392800	Enhancers	Primary B cells from peripheral blood	blood
35	chr5:124392200-124392800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:124392200-124393400	Enhancers	Fetal Stomach	stomach
37	chr5:124392200-124394000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr5:124392200-124394200	Enhancers	Brain Hippocampus Middle	brain
39	chr5:124392200-124394600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:124392200-124395600	Enhancers	HMEC	breast
41	chr5:124392200-124395600	Enhancers	Osteobl	bone
42	chr5:124392200-124396000	Enhancers	H9 Cell Line	embryonic stem cell
43	chr5:124392200-124396400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links