Variant report

Variant	rs28401367
Chromosome Location	chr4:152120229-152120230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152116628..152118796-chr4:152119298..152121521,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10005764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10016856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10028324	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11099784	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027541	1.00[EUR][1000 genomes]
rs17027575	1.00[EUR][1000 genomes]
rs28399915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28432996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28493533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28566074	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28594255	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28644282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28658039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28791569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28836884	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56681758	1.00[EUR][1000 genomes]
rs58001315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58602547	1.00[EUR][1000 genomes]
rs60001201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60661732	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6812606	1.00[AMR][1000 genomes]
rs6820298	1.00[EUR][1000 genomes]
rs6855493	1.00[EUR][1000 genomes]
rs6856037	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72967593	1.00[EUR][1000 genomes]
rs73859998	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73860000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73861187	1.00[EUR][1000 genomes]
rs73861286	1.00[EUR][1000 genomes]
rs7658238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7659047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9918061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997354	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv870229	chr4:152114410-152161072	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152096800-152120600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:152097200-152123600	Weak transcription	Pancreas	Pancrea
3	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
4	chr4:152097400-152123600	Weak transcription	Aorta	Aorta
5	chr4:152097600-152128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:152112400-152120600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:152113400-152124400	Weak transcription	Fetal Intestine Small	intestine
9	chr4:152115000-152124000	Weak transcription	Psoas Muscle	Psoas
10	chr4:152116600-152120400	Weak transcription	Ovary	ovary
11	chr4:152116600-152120600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:152117200-152120400	Enhancers	Brain Angular Gyrus	brain
13	chr4:152117400-152120400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:152117600-152120600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:152117600-152120600	Weak transcription	Lung	lung
16	chr4:152117600-152121400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:152117600-152123200	Weak transcription	Placenta	Placenta
18	chr4:152117600-152123600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:152117600-152124000	Weak transcription	NH-A	brain
20	chr4:152117600-152124200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:152117600-152124400	Weak transcription	A549	lung
22	chr4:152117600-152148800	Weak transcription	Esophagus	oesophagus
23	chr4:152118400-152120600	Weak transcription	Left Ventricle	heart
24	chr4:152118400-152120600	Weak transcription	Small Intestine	intestine
25	chr4:152118600-152120400	Enhancers	Adipose Nuclei	Adipose
26	chr4:152118600-152120600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:152118600-152124200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:152118600-152124200	Weak transcription	Stomach Mucosa	stomach
29	chr4:152118800-152120400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:152118800-152120400	Weak transcription	Brain Anterior Caudate	brain
31	chr4:152118800-152120400	Weak transcription	Osteobl	bone
32	chr4:152118800-152120600	Weak transcription	Right Atrium	heart
33	chr4:152118800-152123400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:152118800-152123400	Weak transcription	HSMM	muscle
35	chr4:152118800-152146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:152119000-152121600	Enhancers	NHDF-Ad	bronchial
37	chr4:152119000-152123400	Weak transcription	HSMMtube	muscle
38	chr4:152119000-152124000	Weak transcription	HUVEC	blood vessel
39	chr4:152119000-152139400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:152119200-152129000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:152119400-152122400	Enhancers	Brain Substantia Nigra	brain
42	chr4:152119400-152139400	Weak transcription	NHEK	skin
43	chr4:152119600-152120600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:152119600-152120800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:152119600-152122400	Enhancers	Fetal Lung	lung
46	chr4:152119800-152120600	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr4:152119800-152120800	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr4:152119800-152121000	Enhancers	Brain Germinal Matrix	brain
49	chr4:152119800-152121400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr4:152119800-152123400	Weak transcription	Placenta Amnion	Placenta Amnion

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