Variant report

Variant	rs2249306
Chromosome Location	chr4:48904835-48904836
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	chr4:48900749..48905906-chr4:48906266..48908973,4	MCF-7	breast:
2	chr4:48782032..48783613-chr4:48903131..48904910,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction
ENSG00000145247	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2243811	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2354945	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2354946	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2572336	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2572346	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2572348	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2572349	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2605234	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2605241	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2605242	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2605269	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4695410	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4695411	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6447669	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7654550	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7686885	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers 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	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48879400-48907800	Weak transcription	Right Ventricle	heart
2	chr4:48890600-48906200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:48891200-48907800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:48891200-48907800	Weak transcription	Fetal Lung	lung
5	chr4:48891400-48907800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:48892000-48905400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr4:48892200-48906600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:48892200-48907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:48892400-48906800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:48892600-48906800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr4:48892800-48907000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:48893000-48906800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:48893200-48908000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:48893400-48905200	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr4:48893800-48907800	Weak transcription	Adipose Nuclei	Adipose
16	chr4:48894000-48907800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:48895000-48908000	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:48895400-48905000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:48895800-48906600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:48896400-48906400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:48896800-48906800	Strong transcription	Fetal Intestine Large	intestine
22	chr4:48897000-48907000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:48897800-48906200	Weak transcription	Fetal Brain Male	brain
24	chr4:48897800-48908000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:48898600-48905400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:48899400-48907600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:48899600-48907000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:48899600-48907800	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:48899800-48908000	Weak transcription	Small Intestine	intestine
30	chr4:48900600-48905000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:48900600-48906800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr4:48900800-48906400	Genic enhancers	Primary T cells from cord blood	blood
33	chr4:48901000-48906400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr4:48901000-48907000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:48901200-48906600	Genic enhancers	NHEK	skin
36	chr4:48901200-48906800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr4:48901200-48906800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:48901200-48907400	Strong transcription	Primary B cells from cord blood	blood
39	chr4:48901400-48905200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:48901400-48905400	Strong transcription	Fetal Brain Female	brain
41	chr4:48901400-48906800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr4:48901400-48906800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:48901400-48907200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:48901600-48905600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:48901600-48906800	Strong transcription	Brain Germinal Matrix	brain
46	chr4:48901800-48907000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:48901800-48907400	Weak transcription	Fetal Heart	heart
48	chr4:48902000-48905000	Strong transcription	Fetal Stomach	stomach
49	chr4:48902000-48906200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:48902000-48906600	Weak transcription	Muscle Satellite Cultured Cells	--

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