Variant report

Variant	rs11542053
Chromosome Location	chr4:82347658-82347659
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:82341740..82344236-chr4:82345813..82347931,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1014409	0.87[EUR][1000 genomes]
rs17558056	1.00[MEX][hapmap]
rs1986163	0.87[EUR][1000 genomes]
rs41470747	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829985	chr4:82199328-82353656	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv4404	chr4:82340986-82386148	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv829986	chr4:82345163-82509860	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82339400-82350000	Weak transcription	Gastric	stomach
2	chr4:82341000-82350600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:82342400-82348600	Enhancers	NHEK	skin
4	chr4:82342600-82349600	Enhancers	Brain Cingulate Gyrus	brain
5	chr4:82342800-82349200	Enhancers	Brain Substantia Nigra	brain
6	chr4:82342800-82353000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:82342800-82366600	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:82343000-82348200	Weak transcription	NH-A	brain
9	chr4:82343000-82348800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:82343000-82350200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:82343000-82351400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:82343200-82348200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:82343200-82348400	Weak transcription	Small Intestine	intestine
14	chr4:82343200-82350200	Weak transcription	Pancreas	Pancrea
15	chr4:82343400-82348200	Weak transcription	Left Ventricle	heart
16	chr4:82343400-82348400	Weak transcription	Lung	lung
17	chr4:82343400-82350000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:82343400-82350200	Weak transcription	Colonic Mucosa	Colon
19	chr4:82343400-82350200	Weak transcription	Right Ventricle	heart
20	chr4:82343400-82350400	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:82343600-82348400	Enhancers	Brain Hippocampus Middle	brain
22	chr4:82343600-82350000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:82344000-82350800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:82344200-82350600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:82344600-82348600	Weak transcription	Brain Germinal Matrix	brain
26	chr4:82344600-82349000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr4:82344600-82349600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr4:82345000-82348000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:82345200-82348400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:82345400-82348200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:82345400-82348600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr4:82345400-82349400	Genic enhancers	Fetal Stomach	stomach
33	chr4:82345400-82350400	Weak transcription	Fetal Brain Female	brain
34	chr4:82345600-82348400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr4:82345600-82352400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:82345600-82352600	Weak transcription	Dnd41	blood
37	chr4:82345600-82356000	Strong transcription	Primary B cells from cord blood	blood
38	chr4:82345600-82380600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:82345800-82350600	Weak transcription	Spleen	Spleen
40	chr4:82345800-82351600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr4:82345800-82361400	Weak transcription	Stomach Mucosa	stomach
42	chr4:82345800-82367600	Strong transcription	Liver	Liver
43	chr4:82345800-82385800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:82346000-82352600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:82346200-82348200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:82346200-82349000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr4:82346200-82352200	Strong transcription	Thymus	Thymus
48	chr4:82346200-82356000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr4:82346200-82356200	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:82346200-82375800	Strong transcription	Primary B cells from peripheral blood	blood

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