Variant report

Variant	rs2553372
Chromosome Location	chr4:124525142-124525143
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	chr4:124524644..124527323-chr4:144255705..144257566,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1452732	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17752451	0.97[ASN][1000 genomes]
rs17809071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993190	0.84[ASN][1000 genomes]
rs2014110	0.81[ASN][1000 genomes]
rs2553360	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2553363	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2553373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553374	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2553375	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2553377	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2553378	0.91[ASN][1000 genomes]
rs2589836	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589865	0.97[ASN][1000 genomes]
rs2893051	0.92[ASN][1000 genomes]
rs4254791	0.80[ASN][1000 genomes]
rs4254792	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4286523	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4365740	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4377602	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4400004	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4596251	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4833280	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4833282	0.97[ASN][1000 genomes]
rs4833931	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534412	0.84[ASN][1000 genomes]
rs6534414	0.95[ASN][1000 genomes]
rs6813552	0.97[ASN][1000 genomes]
rs6838729	0.97[ASN][1000 genomes]
rs7694928	0.83[ASN][1000 genomes]
rs979998	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv879871	chr4:124437842-124527958	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv879872	chr4:124441989-124527958	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv469710	chr4:124474286-124623722	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv482747	chr4:124474286-124623722	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv830047	chr4:124504051-124699142	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124519400-124525200	Enhancers	Fetal Intestine Large	intestine
2	chr4:124519600-124525200	Enhancers	Fetal Intestine Small	intestine
3	chr4:124522000-124528000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr4:124522000-124528000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:124522400-124527600	Weak transcription	NHDF-Ad	bronchial
6	chr4:124522600-124527600	Weak transcription	Adipose Nuclei	Adipose
7	chr4:124522800-124525600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:124522800-124527400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:124522800-124527600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:124523400-124525400	Enhancers	Fetal Thymus	thymus
11	chr4:124524600-124527400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:124524600-124527400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:124524600-124527600	Weak transcription	Primary T cells from cord blood	blood
14	chr4:124524600-124527600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:124524600-124527800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:124524600-124527800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:124524600-124527800	Weak transcription	K562	blood
18	chr4:124524800-124527400	Weak transcription	Small Intestine	intestine
19	chr4:124524800-124527600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:124524800-124527600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:124524800-124527600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:124524800-124529400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:124525000-124526800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:124525000-124528000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:124525000-124528000	Weak transcription	Dnd41	blood

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