Variant report

Variant	rs580223
Chromosome Location	chr11:57541120-57541121
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57506998..57509291-chr11:57540443..57545321,4	K562	blood:
2	chr11:57477927..57479766-chr11:57539022..57541823,2	MCF-7	breast:
3	chr11:57540282..57543092-chr11:57543604..57545694,2	K562	blood:
4	chr11:57540348..57543144-chr11:57545793..57547381,2	K562	blood:

Variant related genes	Relation type
ENSG00000156603	Chromatin interaction
ENSG00000211450	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11229115	0.82[EUR][1000 genomes]
rs483030	0.84[EUR][1000 genomes]
rs486995	0.82[EUR][1000 genomes]
rs501054	0.84[EUR][1000 genomes]
rs501738	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs507946	0.81[EUR][1000 genomes]
rs511708	0.82[EUR][1000 genomes]
rs530094	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs537627	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs541245	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs558653	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs567017	0.84[EUR][1000 genomes]
rs581217	0.83[EUR][1000 genomes]
rs612688	0.83[EUR][1000 genomes]
rs61888880	0.82[EUR][1000 genomes]
rs656227	0.81[EUR][1000 genomes]
rs72928102	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv327	chr11:57532641-57550746	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs580223	MED19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57530400-57545800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr11:57531400-57543200	Weak transcription	Primary B cells from cord blood	blood
3	chr11:57531800-57543200	Weak transcription	Thymus	Thymus
4	chr11:57532800-57541800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:57532800-57543200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:57533200-57541600	Weak transcription	Hela-S3	cervix
7	chr11:57533400-57543000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:57533600-57541200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:57533600-57541800	Weak transcription	Colonic Mucosa	Colon
10	chr11:57533800-57541400	Weak transcription	Fetal Kidney	kidney
11	chr11:57534000-57542600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:57534200-57541600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr11:57534200-57541600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr11:57534200-57542400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:57534200-57542600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:57534400-57542200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:57534800-57542000	Weak transcription	Fetal Stomach	stomach
18	chr11:57535000-57541400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:57535000-57542800	Weak transcription	Brain Germinal Matrix	brain
20	chr11:57535200-57541400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:57535200-57542400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:57535200-57542600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:57535200-57543000	Weak transcription	Fetal Brain Female	brain
24	chr11:57537200-57541800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:57537400-57542800	Weak transcription	Fetal Brain Male	brain
26	chr11:57537600-57541600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:57538400-57546000	Enhancers	Small Intestine	intestine
28	chr11:57538400-57549800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:57538600-57543000	Weak transcription	Fetal Thymus	thymus
30	chr11:57538600-57543200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr11:57538600-57543400	Weak transcription	Primary T cells from cord blood	blood
32	chr11:57538600-57545000	Enhancers	Liver	Liver
33	chr11:57538800-57541800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr11:57538800-57542600	Enhancers	Adipose Nuclei	Adipose
35	chr11:57539000-57541600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:57539000-57541800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr11:57539200-57541200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:57539200-57542600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:57539200-57543400	Weak transcription	Aorta	Aorta
40	chr11:57539200-57543400	Enhancers	Left Ventricle	heart
41	chr11:57539200-57544000	Enhancers	HepG2	liver
42	chr11:57539600-57541600	Weak transcription	Fetal Intestine Small	intestine
43	chr11:57539600-57543200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr11:57539600-57552000	Enhancers	Placenta	Placenta
45	chr11:57539800-57543000	Enhancers	Brain Hippocampus Middle	brain
46	chr11:57539800-57543200	Enhancers	Fetal Heart	heart
47	chr11:57540000-57541600	Weak transcription	Brain Angular Gyrus	brain
48	chr11:57540000-57542400	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:57540000-57542800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:57540200-57541400	Enhancers	A549	lung

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