Variant report

Variant	rs41278071
Chromosome Location	chr4:120488167-120488168
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	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: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10518332	0.81[AMR][1000 genomes]
rs10518333	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12331661	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17007472	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17355550	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17357002	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17357499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17358475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4102980	0.86[AMR][1000 genomes]
rs58735454	0.86[AMR][1000 genomes];0.82[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	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:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
2	chr4:120456200-120488800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:120459400-120491600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:120465000-120489600	Weak transcription	Lung	lung
5	chr4:120472800-120491200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:120472800-120491400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:120478600-120501000	Weak transcription	Fetal Stomach	stomach
8	chr4:120481800-120489200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:120482400-120488200	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:120485000-120493000	Weak transcription	Left Ventricle	heart
11	chr4:120485600-120494600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:120485800-120488200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:120485800-120503800	Weak transcription	Aorta	Aorta
14	chr4:120485800-120520000	Weak transcription	Small Intestine	intestine
15	chr4:120486000-120490800	Weak transcription	NHDF-Ad	bronchial
16	chr4:120486200-120488200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr4:120486200-120488400	Strong transcription	NHLF	lung
18	chr4:120486200-120488600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:120486200-120489600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:120486200-120490400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:120486200-120491600	Weak transcription	Fetal Kidney	kidney
22	chr4:120486200-120503800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:120486200-120504800	Weak transcription	NH-A	brain
24	chr4:120486400-120488200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:120486400-120488200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:120486400-120488200	Strong transcription	Osteobl	bone
27	chr4:120486400-120488400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:120486400-120489600	Weak transcription	Adipose Nuclei	Adipose
29	chr4:120486400-120490800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:120486400-120491600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:120486400-120491800	Weak transcription	Fetal Intestine Large	intestine
32	chr4:120486600-120488800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:120486600-120491400	Weak transcription	Ovary	ovary
34	chr4:120486600-120502800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:120486600-120516600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:120486800-120503600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:120486800-120515800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:120486800-120516400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:120487400-120488400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:120487600-120488200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr4:120487600-120489200	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:120488000-120488200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:120488000-120490800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr4:120488000-120491000	Weak transcription	Fetal Lung	lung
46	chr4:120488000-120491200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr4:120488000-120491400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:120488000-120501000	Weak transcription	Fetal Muscle Leg	muscle

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