Variant report

Variant	rs2288450
Chromosome Location	chr19:41209177-41209178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:41208274-41211010	A549	lung:	n/a	chr19:41208637-41208647 chr19:41208635-41208651 chr19:41208634-41208652
2	BHLHE40	chr19:41208460-41209265	K562	blood:	n/a	chr19:41208759-41208775 chr19:41209120-41209129 chr19:41209117-41209130 chr19:41209119-41209128 chr19:41209119-41209128

No.	Distal block	Cell Line	Cell type
1	chr19:41193182..41199089-chr19:41206241..41209564,9	MCF-7	breast:
2	chr19:41205738..41209357-chr19:41220858..41225801,5	MCF-7	breast:
3	chr19:41195052..41198475-chr19:41206836..41210574,5	K562	blood:
4	chr19:41208433..41210229-chr19:41238150..41240241,2	MCF-7	breast:
5	chr19:41207625..41210988-chr19:41219962..41222313,4	K562	blood:
6	chr19:41208512..41210221-chr19:41220019..41222552,2	MCF-7	breast:
7	chr19:41193560..41201987-chr19:41206623..41212331,16	K562	blood:
8	chr19:41206346..41208282-chr19:41208723..41211449,2	K562	blood:
9	chr19:41204060..41206882-chr19:41209146..41210846,2	MCF-7	breast:
10	chr19:41207302..41211180-chr19:41220761..41224340,7	K562	blood:
11	chr19:41207886..41210278-chr19:41305758..41307658,2	K562	blood:

Variant related genes	Relation type
ADCK4	TF binding region
ENSG00000269858	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000105245	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10404911	0.82[EUR][1000 genomes]
rs10426415	0.82[EUR][1000 genomes]
rs28493229	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3745213	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3815912	0.83[EUR][1000 genomes]
rs59459325	0.82[EUR][1000 genomes]
rs73546894	0.81[EUR][1000 genomes]
rs73931345	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	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
4	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41197200-41210000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr19:41197200-41210600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:41197200-41220200	Weak transcription	Fetal Heart	heart
4	chr19:41197200-41220600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:41197400-41210600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:41197400-41219800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:41197400-41220000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:41197400-41220000	Strong transcription	Fetal Intestine Small	intestine
9	chr19:41197400-41220200	Weak transcription	HUVEC	blood vessel
10	chr19:41197600-41216000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr19:41197600-41220200	Weak transcription	Psoas Muscle	Psoas
12	chr19:41197800-41211000	Weak transcription	Right Atrium	heart
13	chr19:41197800-41219000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr19:41198400-41219800	Weak transcription	NH-A	brain
15	chr19:41199000-41217600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:41200200-41211800	Strong transcription	Ovary	ovary
17	chr19:41200400-41209400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:41201800-41209800	Weak transcription	Hela-S3	cervix
19	chr19:41204200-41212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:41204200-41219800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:41204400-41210800	Strong transcription	Left Ventricle	heart
22	chr19:41204400-41211200	Strong transcription	Adipose Nuclei	Adipose
23	chr19:41204400-41211600	Strong transcription	Fetal Brain Female	brain
24	chr19:41204400-41212400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr19:41204400-41212600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr19:41204400-41212800	Strong transcription	Brain Germinal Matrix	brain
27	chr19:41204400-41213800	Strong transcription	Lung	lung
28	chr19:41204400-41215800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:41204400-41216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:41204400-41219000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr19:41204600-41210800	Strong transcription	Fetal Muscle Leg	muscle
32	chr19:41204600-41212400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:41204600-41217400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:41204600-41217800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:41204600-41219400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr19:41204800-41211800	Strong transcription	Placenta	Placenta
37	chr19:41204800-41216600	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr19:41205000-41209200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:41205000-41210800	Strong transcription	Right Ventricle	heart
40	chr19:41205000-41213000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr19:41205000-41216800	Strong transcription	Thymus	Thymus
42	chr19:41205000-41217800	Strong transcription	Fetal Thymus	thymus
43	chr19:41205000-41219000	Strong transcription	Fetal Intestine Large	intestine
44	chr19:41205200-41210800	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:41205200-41211000	Strong transcription	Osteobl	bone
46	chr19:41205200-41211800	Strong transcription	Colonic Mucosa	Colon
47	chr19:41205200-41212400	Strong transcription	Brain Anterior Caudate	brain
48	chr19:41205200-41212600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr19:41205200-41212800	Strong transcription	Brain Cingulate Gyrus	brain
50	chr19:41205200-41218800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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