Variant report

Variant	rs11946293
Chromosome Location	chr4:88112940-88112941
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88112029..88115126-chr4:88139994..88142712,4	MCF-7	breast:
2	chr4:88112928..88115867-chr4:88140450..88142503,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10000784	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10025704	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1021104	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13435265	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1481947	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1552144	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17012516	0.82[AMR][1000 genomes]
rs17012517	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28505236	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28571134	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28670747	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28734493	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28882732	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3193672	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3209390	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4577539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55747890	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66527077	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72667790	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7437661	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[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	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 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	chr4:88068000-88116400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr4:88073400-88113000	Weak transcription	NHDF-Ad	bronchial
3	chr4:88081800-88140200	Weak transcription	Aorta	Aorta
4	chr4:88082000-88129200	Weak transcription	Esophagus	oesophagus
5	chr4:88082600-88120000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr4:88083000-88116400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:88084800-88113600	Weak transcription	HSMM	muscle
8	chr4:88085000-88128000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:88089600-88113600	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:88089600-88131000	Weak transcription	Ovary	ovary
11	chr4:88089800-88115800	Weak transcription	HepG2	liver
12	chr4:88090000-88118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:88091400-88118200	Weak transcription	Brain Anterior Caudate	brain
14	chr4:88091800-88115000	Weak transcription	Left Ventricle	heart
15	chr4:88091800-88128000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:88091800-88128600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:88091800-88133600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:88092200-88134800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:88093000-88113200	Weak transcription	K562	blood
20	chr4:88093800-88113400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:88093800-88119600	Weak transcription	Primary T cells from cord blood	blood
22	chr4:88096800-88115400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:88097600-88125200	Weak transcription	Primary B cells from cord blood	blood
24	chr4:88097600-88140400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:88098000-88114800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:88098000-88127400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:88098800-88115600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:88099000-88118400	Weak transcription	Fetal Intestine Large	intestine
29	chr4:88099800-88115200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:88100400-88119200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr4:88106800-88113000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:88108600-88115600	Weak transcription	Gastric	stomach
33	chr4:88109600-88133600	Weak transcription	Fetal Lung	lung
34	chr4:88110200-88113600	Weak transcription	HSMMtube	muscle
35	chr4:88110400-88113600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:88110400-88113600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:88110400-88115200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:88110400-88118400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:88110400-88127600	Weak transcription	Liver	Liver
40	chr4:88110600-88113000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:88110800-88114000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:88110800-88128200	Weak transcription	Fetal Intestine Small	intestine
43	chr4:88111000-88120200	Weak transcription	Fetal Kidney	kidney

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