Variant report

Variant	rs543844
Chromosome Location	chr6:44424800-44424801
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44424482..44427083-chr6:44435106..44437483,2	K562	blood:
2	chr6:44423031..44426172-chr6:44427931..44431207,4	K562	blood:
3	chr6:44398593..44399479-chr6:44423901..44425088,5	MCF-7	breast:
4	chr6:44423082..44425791-chr6:44432215..44434664,2	K562	blood:

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4714789	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs517214	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557944	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs566078	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs928341	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant related diseases (count:1)

Disease	PMID	Source
Migraine	23793025	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs543844	TCTE1	cis	parietal	SCAN
rs543844	CD2AP	cis	cerebellum	SCAN
rs543844	MED20	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44396600-44432800	Weak transcription	Fetal Kidney	kidney
2	chr6:44412000-44425800	Weak transcription	Esophagus	oesophagus
3	chr6:44413600-44427600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:44416200-44432400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:44416400-44430800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:44419400-44428200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:44420600-44425600	Weak transcription	Fetal Thymus	thymus
8	chr6:44420600-44430200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:44420800-44424800	Weak transcription	A549	lung
10	chr6:44420800-44425000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:44420800-44430600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:44420800-44432400	Weak transcription	Fetal Lung	lung
13	chr6:44421200-44425400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:44422400-44425400	Weak transcription	Fetal Brain Male	brain
15	chr6:44422400-44431800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:44422400-44432000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:44424200-44424800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:44424200-44425000	Enhancers	Fetal Heart	heart
19	chr6:44424200-44425000	Flanking Active TSS	HUVEC	blood vessel
20	chr6:44424200-44425200	Flanking Active TSS	K562	blood
21	chr6:44424400-44424800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr6:44424400-44424800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:44424400-44424800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:44424400-44424800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr6:44424400-44424800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:44424400-44424800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:44424400-44424800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr6:44424400-44424800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:44424400-44424800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:44424400-44424800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:44424400-44424800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:44424400-44424800	Enhancers	Adipose Nuclei	Adipose
33	chr6:44424400-44424800	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr6:44424400-44424800	Enhancers	Colonic Mucosa	Colon
35	chr6:44424400-44424800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr6:44424400-44424800	Enhancers	Fetal Muscle Leg	muscle
37	chr6:44424400-44424800	Enhancers	Left Ventricle	heart
38	chr6:44424400-44424800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr6:44424400-44424800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr6:44424400-44424800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr6:44424400-44424800	Enhancers	Stomach Mucosa	stomach
42	chr6:44424400-44424800	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr6:44424400-44424800	Flanking Active TSS	HSMM	muscle
44	chr6:44424400-44424800	Enhancers	HSMMtube	muscle
45	chr6:44424400-44424800	Flanking Active TSS	NHEK	skin
46	chr6:44424400-44424800	Enhancers	NHLF	lung
47	chr6:44424400-44424800	Flanking Active TSS	Osteobl	bone
48	chr6:44424400-44425000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:44424400-44425000	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr6:44424400-44425000	Enhancers	HUES64 Cell Line	embryonic stem cell

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