Variant report

Variant	rs55800109
Chromosome Location	chr12:50583357-50583358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50477100..50479136-chr12:50582674..50585443,2	K562	blood:
2	chr12:50574926..50577485-chr12:50582740..50584588,2	K562	blood:
3	chr12:50583119..50586019-chr12:50610359..50613018,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CERS5-1	chr12:50579363-50584044	ENSG00000257298.1

Variant related genes	Relation type
ENSG00000066117	Chromatin interaction
ENSG00000257531	Chromatin interaction
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11169272	1.00[AMR][1000 genomes]
rs11169273	1.00[AMR][1000 genomes]
rs11169279	1.00[AMR][1000 genomes]
rs11169280	1.00[AMR][1000 genomes]
rs12299109	1.00[AMR][1000 genomes]
rs12305438	1.00[AMR][1000 genomes]
rs12309501	1.00[AMR][1000 genomes]
rs296738	1.00[AMR][1000 genomes]
rs296753	1.00[AMR][1000 genomes]
rs372753	1.00[AMR][1000 genomes]
rs57143574	1.00[AMR][1000 genomes]
rs57596053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58826760	1.00[AMR][1000 genomes]
rs61221429	1.00[AMR][1000 genomes]
rs672697	1.00[AMR][1000 genomes]
rs7312996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74090092	1.00[AMR][1000 genomes]
rs74090094	1.00[AMR][1000 genomes]
rs74090112	1.00[AMR][1000 genomes]
rs74092539	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7963427	0.82[AFR][1000 genomes];1.00[AMR][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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50562000-50584800	Weak transcription	K562	blood
2	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:50564400-50586200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:50570400-50592800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:50570800-50589800	Strong transcription	Fetal Stomach	stomach
8	chr12:50571800-50586000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:50571800-50586200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:50571800-50595800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:50571800-50597000	Weak transcription	Thymus	Thymus
12	chr12:50571800-50597600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:50572000-50586000	Weak transcription	Left Ventricle	heart
15	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
16	chr12:50572600-50586200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:50575600-50586000	Weak transcription	Dnd41	blood
18	chr12:50575800-50585000	Weak transcription	Liver	Liver
19	chr12:50575800-50586000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:50576000-50584600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:50576000-50584600	Weak transcription	Fetal Thymus	thymus
22	chr12:50576000-50586200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:50576600-50595000	Weak transcription	A549	lung
24	chr12:50577800-50583400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:50578600-50586200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:50578800-50583400	Genic enhancers	Adipose Nuclei	Adipose
27	chr12:50578800-50583400	Genic enhancers	HMEC	breast
28	chr12:50578800-50585200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:50579000-50583600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:50579200-50584200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:50579600-50583400	Enhancers	Brain Germinal Matrix	brain
32	chr12:50579600-50583400	Genic enhancers	NHLF	lung
33	chr12:50579600-50584600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:50579600-50598000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:50579800-50583600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:50580200-50583600	Enhancers	HepG2	liver
37	chr12:50580400-50583600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:50580400-50595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:50580600-50585200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:50581200-50583400	Genic enhancers	Rectal Mucosa Donor 29	rectum
41	chr12:50581200-50583600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:50581400-50583400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:50581400-50583400	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr12:50581400-50583400	Genic enhancers	HUVEC	blood vessel
45	chr12:50581400-50583600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:50581600-50583400	Genic enhancers	Fetal Intestine Small	intestine
47	chr12:50581600-50583400	Genic enhancers	NH-A	brain
48	chr12:50581600-50583600	Genic enhancers	Fetal Intestine Large	intestine
49	chr12:50581600-50584600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:50581800-50583400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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