Variant report

Variant	rs13405281
Chromosome Location	chr2:58323726-58323727
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	chr2:58322239..58324649-chr2:58364726..58366691,2	MCF-7	breast:
2	chr2:58273263..58275432-chr2:58322196..58325090,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10165760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10174202	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10176681	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10178025	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10182762	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10187411	0.82[AFR][1000 genomes]
rs10203014	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1025755	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11883874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11891477	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11892302	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900900	0.89[AMR][1000 genomes]
rs12104650	0.81[AFR][1000 genomes]
rs12105064	0.81[AMR][1000 genomes]
rs13382369	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13394820	0.95[AFR][1000 genomes]
rs13397947	0.89[AMR][1000 genomes]
rs13410228	0.82[AFR][1000 genomes]
rs13410500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13419989	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13431271	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1371213	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2165100	0.93[AFR][1000 genomes]
rs2165103	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2312486	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28521626	0.95[AFR][1000 genomes]
rs4459722	0.89[AFR][1000 genomes]
rs57112138	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57597086	0.83[AFR][1000 genomes]
rs58470176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60364084	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6718190	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6740373	0.89[AMR][1000 genomes]
rs6740836	0.89[AMR][1000 genomes]
rs6742445	0.89[AMR][1000 genomes]
rs716758	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948876	0.89[AMR][1000 genomes]
rs72949131	0.82[AFR][1000 genomes]
rs72949137	0.92[AFR][1000 genomes]
rs72951042	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7340170	0.89[AMR][1000 genomes]
rs73944804	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7563312	0.84[AFR][1000 genomes]
rs7569184	0.81[AMR][1000 genomes]
rs7569731	0.87[AFR][1000 genomes]
rs7574578	0.89[AMR][1000 genomes]
rs7574694	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7590976	0.89[AMR][1000 genomes]
rs7597069	0.89[AMR][1000 genomes]
rs7600213	0.92[AFR][1000 genomes]
rs9309303	0.89[AMR][1000 genomes]
rs9973345	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9973928	0.98[AFR][1000 genomes];1.00[AMR][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	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58275000-58326600	Weak transcription	Pancreas	Pancrea
2	chr2:58282600-58350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:58284400-58325000	Weak transcription	NHEK	skin
4	chr2:58291600-58325000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:58303000-58358800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:58307600-58328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:58308600-58333600	Weak transcription	NHDF-Ad	bronchial
8	chr2:58309400-58324400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:58310400-58326000	Weak transcription	Hela-S3	cervix
10	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
11	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:58316600-58326200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:58318200-58327600	Weak transcription	Placenta	Placenta
14	chr2:58318200-58373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:58318400-58334800	Weak transcription	HSMM	muscle
16	chr2:58318800-58325400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:58319400-58358400	Weak transcription	Ovary	ovary
18	chr2:58319600-58326600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:58319800-58325000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:58319800-58325000	Weak transcription	HMEC	breast
21	chr2:58319800-58325400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:58319800-58325400	Weak transcription	Osteobl	bone
23	chr2:58319800-58326000	Weak transcription	K562	blood
24	chr2:58319800-58326200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:58319800-58349800	Weak transcription	Primary T cells from cord blood	blood
26	chr2:58319800-58350800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:58319800-58359000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:58319800-58367200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:58320000-58325000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:58320000-58325000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:58320000-58325200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:58320000-58326400	Weak transcription	Primary B cells from cord blood	blood
33	chr2:58320000-58326600	Weak transcription	Psoas Muscle	Psoas
34	chr2:58320000-58327600	Weak transcription	Fetal Lung	lung
35	chr2:58320000-58334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:58320000-58334600	Weak transcription	HUVEC	blood vessel
37	chr2:58320000-58334800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:58320000-58339600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:58320000-58347600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:58320000-58359000	Weak transcription	Left Ventricle	heart
41	chr2:58322200-58325000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:58322200-58334200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:58322200-58347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:58322600-58334400	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:58322600-58349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:58322600-58350400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr2:58323200-58324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:58323200-58335400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:58323200-58347600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:58323200-58350400	Weak transcription	Primary T cells fromperipheralblood	blood

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