Variant report

Variant	rs28626938
Chromosome Location	chr4:120486445-120486446
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	chr4:120485362..120487909-chr4:120507957..120510627,2	K562	blood:
2	chr4:120486128..120488621-chr4:120988005..120990229,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164109	Chromatin interaction
ENSG00000250938	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10003668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10016736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10021823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10213673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17007576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28372207	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28590372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28622960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7694856	1.00[AFR][1000 genomes];1.00[AMR][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
2	chr4:120435000-120487600	Weak transcription	Colonic Mucosa	Colon
3	chr4:120456200-120488800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:120459400-120491600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:120465000-120489600	Weak transcription	Lung	lung
6	chr4:120472800-120491200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:120472800-120491400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:120473800-120487800	Weak transcription	Placenta	Placenta
9	chr4:120478600-120501000	Weak transcription	Fetal Stomach	stomach
10	chr4:120481800-120489200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:120482400-120488200	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:120483400-120486800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:120483400-120487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:120483800-120487800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:120484400-120486600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:120484600-120486600	ZNF genes & repeats	Fetal Lung	lung
17	chr4:120484600-120486800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr4:120484600-120487000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
19	chr4:120484800-120486600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
20	chr4:120484800-120486600	Strong transcription	Rectal Smooth Muscle	rectum
21	chr4:120484800-120486800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr4:120485000-120493000	Weak transcription	Left Ventricle	heart
23	chr4:120485400-120486600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr4:120485400-120486800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
25	chr4:120485400-120486800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr4:120485600-120486600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:120485600-120486600	ZNF genes & repeats	Colon Smooth Muscle	Colon
28	chr4:120485600-120486600	Strong transcription	Ovary	ovary
29	chr4:120485600-120494600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:120485800-120486800	Weak transcription	Fetal Brain Male	brain
31	chr4:120485800-120487600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:120485800-120487800	Weak transcription	Fetal Heart	heart
33	chr4:120485800-120488200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:120485800-120503800	Weak transcription	Aorta	Aorta
35	chr4:120485800-120520000	Weak transcription	Small Intestine	intestine
36	chr4:120486000-120486600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:120486000-120486600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:120486000-120490800	Weak transcription	NHDF-Ad	bronchial
39	chr4:120486200-120486600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr4:120486200-120487400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:120486200-120488000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:120486200-120488200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr4:120486200-120488400	Strong transcription	NHLF	lung
44	chr4:120486200-120488600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:120486200-120489600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:120486200-120490400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:120486200-120491600	Weak transcription	Fetal Kidney	kidney
48	chr4:120486200-120503800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:120486200-120504800	Weak transcription	NH-A	brain
50	chr4:120486400-120486600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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