Variant report

Variant	rs2604888
Chromosome Location	chr19:41213030-41213031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41210809..41213547-chr19:41214438..41217291,3	K562	blood:
2	chr19:41211245..41213405-chr19:41215813..41217880,2	MCF-7	breast:
3	chr19:41204648..41207445-chr19:41212507..41214384,2	K562	blood:

Variant related genes	Relation type
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11672197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2561528	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2561530	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2604913	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2604888	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41197200-41220200	Weak transcription	Fetal Heart	heart
2	chr19:41197200-41220600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:41197400-41219800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:41197400-41220000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:41197400-41220000	Strong transcription	Fetal Intestine Small	intestine
6	chr19:41197400-41220200	Weak transcription	HUVEC	blood vessel
7	chr19:41197600-41216000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr19:41197600-41220200	Weak transcription	Psoas Muscle	Psoas
9	chr19:41197800-41219000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr19:41198400-41219800	Weak transcription	NH-A	brain
11	chr19:41199000-41217600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:41204200-41219800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:41204400-41213800	Strong transcription	Lung	lung
14	chr19:41204400-41215800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:41204400-41216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:41204400-41219000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr19:41204600-41217400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:41204600-41217800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:41204600-41219400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr19:41204800-41216600	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:41205000-41216800	Strong transcription	Thymus	Thymus
22	chr19:41205000-41217800	Strong transcription	Fetal Thymus	thymus
23	chr19:41205000-41219000	Strong transcription	Fetal Intestine Large	intestine
24	chr19:41205200-41218800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:41205200-41218800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr19:41205400-41215800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:41205400-41216000	Strong transcription	Primary T cells from cord blood	blood
28	chr19:41205400-41216200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:41205400-41217000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr19:41205400-41218000	Strong transcription	Brain Hippocampus Middle	brain
31	chr19:41205400-41219000	Strong transcription	Liver	Liver
32	chr19:41205400-41219200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:41205400-41220200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr19:41205600-41218800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr19:41205600-41219200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr19:41205800-41219400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:41206000-41213600	Weak transcription	GM12878-XiMat	blood
38	chr19:41206400-41219800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:41207000-41216000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:41207400-41216800	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr19:41208400-41217200	Weak transcription	NHDF-Ad	bronchial
42	chr19:41208600-41220000	Strong transcription	Fetal Stomach	stomach
43	chr19:41208800-41216800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:41208800-41217400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:41208800-41220000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:41208800-41220200	Weak transcription	Stomach Mucosa	stomach
47	chr19:41208800-41221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr19:41209000-41214800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr19:41209000-41219000	Strong transcription	A549	lung
50	chr19:41209200-41219200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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