Variant report

Variant	rs59546292
Chromosome Location	chr22:29339864-29339865
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	chr22:29278303..29280288-chr22:29337849..29340109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11912894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11913224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11913805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55665300	1.00[EUR][1000 genomes]
rs55945584	1.00[EUR][1000 genomes]
rs56089216	1.00[EUR][1000 genomes]
rs56332784	1.00[EUR][1000 genomes]
rs56728146	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57119189	1.00[EUR][1000 genomes]
rs57188271	1.00[EUR][1000 genomes]
rs57198336	1.00[EUR][1000 genomes]
rs57846969	1.00[EUR][1000 genomes]
rs58089713	1.00[EUR][1000 genomes]
rs58162235	1.00[EUR][1000 genomes]
rs58221763	1.00[EUR][1000 genomes]
rs59519868	1.00[EUR][1000 genomes]
rs60003056	1.00[EUR][1000 genomes]
rs6005942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60187407	1.00[EUR][1000 genomes]
rs60747358	1.00[EUR][1000 genomes]
rs60780652	1.00[EUR][1000 genomes]
rs61257487	1.00[EUR][1000 genomes]
rs61581392	1.00[EUR][1000 genomes]
rs722590	1.00[EUR][1000 genomes]
rs7287244	1.00[EUR][1000 genomes]
rs73881187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73881189	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73881197	1.00[EUR][1000 genomes]
rs73881200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73881201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73882404	1.00[EUR][1000 genomes]
rs73882405	1.00[EUR][1000 genomes]
rs73882406	1.00[EUR][1000 genomes]
rs73882414	1.00[EUR][1000 genomes]
rs73882422	1.00[EUR][1000 genomes]
rs73882424	1.00[EUR][1000 genomes]
rs73882428	1.00[EUR][1000 genomes]
rs73882440	1.00[EUR][1000 genomes]
rs73882443	1.00[EUR][1000 genomes]
rs73882445	1.00[EUR][1000 genomes]
rs73882447	1.00[EUR][1000 genomes]
rs73882449	1.00[EUR][1000 genomes]
rs8138963	1.00[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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29314400-29342800	Weak transcription	Brain Substantia Nigra	brain
2	chr22:29331400-29341000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr22:29332000-29343000	Weak transcription	Brain Angular Gyrus	brain
4	chr22:29332600-29347600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:29333800-29347800	Weak transcription	Gastric	stomach
6	chr22:29334400-29340400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:29334600-29342800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr22:29334800-29340000	Enhancers	HepG2	liver
9	chr22:29335400-29340000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr22:29335400-29340000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr22:29335800-29347800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr22:29336200-29347600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr22:29337000-29342000	Weak transcription	A549	lung
14	chr22:29337800-29340000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr22:29337800-29340400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr22:29338200-29340000	Enhancers	Fetal Kidney	kidney
17	chr22:29338200-29340200	Enhancers	Liver	Liver
18	chr22:29338200-29340200	Enhancers	Brain Anterior Caudate	brain
19	chr22:29338400-29340000	Enhancers	Colon Smooth Muscle	Colon
20	chr22:29338600-29347600	Weak transcription	Left Ventricle	heart
21	chr22:29338800-29340000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr22:29338800-29340200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr22:29338800-29340200	Enhancers	Fetal Muscle Leg	muscle
24	chr22:29339000-29340000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr22:29339000-29340200	Enhancers	Fetal Brain Male	brain
26	chr22:29339000-29340200	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr22:29339200-29340000	Enhancers	Fetal Brain Female	brain
28	chr22:29339200-29340000	Enhancers	Stomach Smooth Muscle	stomach
29	chr22:29339400-29340000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:29339400-29340000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr22:29339400-29340000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr22:29339400-29340000	Enhancers	Aorta	Aorta
33	chr22:29339400-29340200	Enhancers	Adipose Nuclei	Adipose
34	chr22:29339400-29340200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr22:29339400-29340200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr22:29339400-29342800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr22:29339600-29340000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr22:29339600-29340000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr22:29339600-29340000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr22:29339600-29340000	Enhancers	HSMMtube	muscle
41	chr22:29339600-29340200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr22:29339600-29342600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr22:29339600-29342600	Weak transcription	Small Intestine	intestine
44	chr22:29339600-29345400	Weak transcription	Lung	lung
45	chr22:29339600-29345600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr22:29339600-29346800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr22:29339600-29347600	Weak transcription	Pancreas	Pancrea
48	chr22:29339800-29340000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr22:29339800-29340200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr22:29339800-29340600	Enhancers	Cortex derived primary cultured neurospheres	brain

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