Variant report

Variant	rs2561536
Chromosome Location	chr19:41236722-41236723
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41223689..41226638-chr19:41236669..41239105,2	K562	blood:
2	chr19:41235808..41237635-chr19:41255740..41258209,2	K562	blood:

Variant related genes	Relation type
ENSG00000188493	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11538385	0.82[JPT][hapmap]
rs1965715	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2561528	0.82[JPT][hapmap]
rs2604913	0.82[JPT][hapmap]
rs2607420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6508945	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2561536	ADCK4	cis	Nerve Tibial	GTEx
rs2561536	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41225200-41238800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41225200-41243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:41226400-41246200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:41226600-41238600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:41226600-41245600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:41226800-41245200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:41226800-41245600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:41226800-41245800	Strong transcription	Fetal Stomach	stomach
9	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:41227200-41237000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart
12	chr19:41228000-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:41228200-41238000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:41228200-41241400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr19:41228200-41246600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr19:41228200-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:41228600-41237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:41228600-41238800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:41228600-41240000	Weak transcription	Stomach Mucosa	stomach
20	chr19:41228600-41240400	Strong transcription	HepG2	liver
21	chr19:41228600-41241200	Strong transcription	A549	lung
22	chr19:41228600-41245400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr19:41228600-41245600	Strong transcription	Fetal Muscle Leg	muscle
24	chr19:41228600-41250000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:41228600-41251000	Strong transcription	Fetal Brain Female	brain
26	chr19:41229200-41240800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:41229200-41246800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:41229200-41247200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:41229400-41241200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr19:41229400-41246800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:41229400-41246800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr19:41229400-41249000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:41229600-41242000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr19:41229600-41244000	Strong transcription	Ovary	ovary
35	chr19:41229600-41245600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr19:41229600-41246800	Strong transcription	Fetal Lung	lung
37	chr19:41229800-41237400	Strong transcription	Primary B cells from cord blood	blood
38	chr19:41229800-41239200	Strong transcription	Spleen	Spleen
39	chr19:41229800-41241200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr19:41229800-41245600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:41229800-41246400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:41229800-41246800	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr19:41229800-41247000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:41229800-41247000	Strong transcription	Liver	Liver
45	chr19:41229800-41247200	Strong transcription	Primary T cells from cord blood	blood
46	chr19:41229800-41248600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:41229800-41248600	Strong transcription	Dnd41	blood
48	chr19:41229800-41249200	Strong transcription	Thymus	Thymus
49	chr19:41229800-41250400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr19:41230000-41240800	Strong transcription	Fetal Intestine Large	intestine

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