Variant report

Variant	rs13400353
Chromosome Location	chr2:55273181-55273182
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55131871..55133906-chr2:55272256..55273757,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10084445	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10170102	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10175952	1.00[CEU][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10179491	0.84[EUR][1000 genomes]
rs10180207	0.90[EUR][1000 genomes]
rs10181115	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10182203	0.92[EUR][1000 genomes]
rs10191748	0.87[AMR][1000 genomes]
rs10191774	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10197533	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10198096	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10206953	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10207701	0.90[AMR][1000 genomes]
rs11125554	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13385999	1.00[CEU][hapmap]
rs13387710	0.90[AMR][1000 genomes]
rs13401780	0.88[EUR][1000 genomes]
rs13416852	0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs17046567	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17046569	1.00[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4358163	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs60989108	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6545469	1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545470	0.88[EUR][1000 genomes]
rs6715980	1.00[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs6744637	0.96[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs6758258	0.93[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs6760773	0.86[EUR][1000 genomes]
rs72912579	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7570298	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7584992	1.00[MEX][hapmap]
rs7592869	0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
2	chr2:55259400-55275200	Weak transcription	Esophagus	oesophagus
3	chr2:55260800-55273200	Weak transcription	Psoas Muscle	Psoas
4	chr2:55266200-55273600	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55266800-55273400	Weak transcription	Fetal Thymus	thymus
6	chr2:55268000-55274800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:55270200-55274000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:55270400-55273400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:55270400-55273600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:55270600-55273400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:55271200-55273200	Active TSS	Fetal Brain Female	brain
12	chr2:55271400-55275000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:55271400-55278200	Active TSS	HSMMtube	muscle
14	chr2:55271600-55273400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr2:55271600-55274600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:55271600-55274800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:55271600-55275000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:55271600-55275000	Weak transcription	Lung	lung
19	chr2:55271600-55275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:55271600-55275200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:55271800-55273400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:55271800-55273600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr2:55272000-55273200	Active TSS	NHLF	lung
24	chr2:55272000-55273600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr2:55272000-55274000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:55272000-55274000	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr2:55272000-55274000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr2:55272000-55274200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:55272000-55274600	Enhancers	Rectal Smooth Muscle	rectum
30	chr2:55272000-55274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr2:55272000-55275000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:55272200-55273400	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr2:55272200-55274000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:55272200-55274600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr2:55272200-55274600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:55272200-55274600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:55272200-55274600	Enhancers	Fetal Lung	lung
38	chr2:55272200-55274800	Enhancers	Fetal Intestine Large	intestine
39	chr2:55272400-55273200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:55272400-55273200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
41	chr2:55272400-55273400	Flanking Active TSS	A549	lung
42	chr2:55272400-55273400	Enhancers	Hela-S3	cervix
43	chr2:55272400-55273600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:55272400-55273800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:55272400-55274400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:55272400-55274600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:55272400-55275000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:55272400-55275000	Flanking Active TSS	HUVEC	blood vessel
49	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:55272600-55273200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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