Variant report

Variant	rs4440005
Chromosome Location	chr2:54807088-54807089
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54806062..54808345-chr2:54823269..54826209,2	MCF-7	breast:
2	chr2:54735530..54737587-chr2:54805600..54807327,2	MCF-7	breast:
3	chr2:54781728..54792106-chr2:54796721..54808716,28	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13389329	0.85[EUR][1000 genomes]
rs17343918	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17344134	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344169	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344176	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344287	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344308	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344343	0.91[EUR][1000 genomes]
rs17415829	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17415857	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17416130	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416291	0.91[EUR][1000 genomes]
rs17521468	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521510	0.91[EUR][1000 genomes]
rs17580255	0.83[EUR][1000 genomes]
rs17580855	0.91[EUR][1000 genomes]
rs17580876	0.91[EUR][1000 genomes]
rs1804472	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796015	1.00[EUR][1000 genomes]
rs41281495	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41281497	0.91[EUR][1000 genomes]
rs4258834	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57810131	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58143357	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59228485	0.82[EUR][1000 genomes]
rs61480394	0.82[EUR][1000 genomes]
rs6755737	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911563	0.82[EUR][1000 genomes]
rs73932787	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54795800-54807600	Enhancers	Duodenum Smooth Muscle	Duodenum
2	chr2:54796000-54807600	Enhancers	Brain Angular Gyrus	brain
3	chr2:54796400-54808800	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr2:54796800-54807400	Enhancers	Psoas Muscle	Psoas
5	chr2:54796800-54810200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr2:54796800-54810600	Enhancers	Small Intestine	intestine
7	chr2:54797400-54808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:54800000-54807400	Enhancers	Right Ventricle	heart
9	chr2:54801600-54808600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:54801800-54807400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:54801800-54811000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:54802000-54808400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr2:54802000-54816400	Enhancers	Liver	Liver
14	chr2:54802200-54822600	Weak transcription	Esophagus	oesophagus
15	chr2:54802400-54808600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:54803000-54807200	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:54803000-54807200	Weak transcription	Dnd41	blood
18	chr2:54803000-54807800	Enhancers	Brain Hippocampus Middle	brain
19	chr2:54803200-54807600	Enhancers	HMEC	breast
20	chr2:54803400-54807200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:54803600-54807200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:54803600-54807200	Enhancers	Brain Substantia Nigra	brain
23	chr2:54803600-54807400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr2:54803600-54808400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:54803800-54807200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr2:54803800-54807200	Enhancers	Stomach Smooth Muscle	stomach
27	chr2:54803800-54807600	Enhancers	Colon Smooth Muscle	Colon
28	chr2:54804000-54807400	Enhancers	Fetal Heart	heart
29	chr2:54804000-54808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:54804000-54809400	Enhancers	Fetal Kidney	kidney
31	chr2:54804000-54822400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:54804200-54807800	Enhancers	Fetal Lung	lung
33	chr2:54804200-54808600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:54804200-54809400	Enhancers	Thymus	Thymus
35	chr2:54804400-54807200	Enhancers	Fetal Intestine Small	intestine
36	chr2:54804400-54807600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:54804400-54807800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:54804400-54808000	Enhancers	Fetal Stomach	stomach
39	chr2:54804600-54809800	Enhancers	Fetal Intestine Large	intestine
40	chr2:54804600-54814600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr2:54804800-54807200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:54804800-54807400	Enhancers	Osteobl	bone
43	chr2:54805000-54807400	Enhancers	Fetal Muscle Leg	muscle
44	chr2:54805000-54807800	Enhancers	Adipose Nuclei	Adipose
45	chr2:54805000-54811000	Enhancers	Fetal Thymus	thymus
46	chr2:54805200-54807800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:54805400-54807800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:54805400-54807800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:54805400-54810400	Enhancers	Primary B cells from peripheral blood	blood
50	chr2:54805400-54815800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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