Variant report

Variant	rs4402455
Chromosome Location	chr14:55337869-55337870
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55336799..55338659-chr14:55514913..55516718,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10133449	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10134163	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10145097	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10146658	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12147422	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17128050	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28477407	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28542181	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28757745	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34429973	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4363780	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57575708	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61702394	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7141319	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7141433	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73280512	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7492600	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010689	0.85[EUR][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	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4402455	GCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55327000-55338200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr14:55329400-55347800	Weak transcription	Primary B cells from cord blood	blood
3	chr14:55330800-55347800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr14:55331800-55344800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr14:55331800-55347600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr14:55332800-55338000	Weak transcription	Small Intestine	intestine
7	chr14:55333200-55343800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr14:55334000-55346200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:55336400-55338400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr14:55336600-55338000	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr14:55336800-55338000	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr14:55336800-55338000	Active TSS	Duodenum Mucosa	Duodenum
13	chr14:55337000-55338000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr14:55337000-55338000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:55337000-55338000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr14:55337000-55338000	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr14:55337000-55338000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr14:55337000-55338000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr14:55337000-55338000	Active TSS	Brain Anterior Caudate	brain
20	chr14:55337000-55338000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr14:55337000-55338000	Active TSS	Colonic Mucosa	Colon
22	chr14:55337000-55338000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr14:55337000-55338000	Active TSS	Fetal Intestine Small	intestine
24	chr14:55337000-55338000	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr14:55337000-55338000	Active TSS	Stomach Smooth Muscle	stomach
26	chr14:55337000-55343600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr14:55337200-55345000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr14:55337400-55338000	Active TSS	Fetal Stomach	stomach
29	chr14:55337400-55346000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr14:55337400-55346200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr14:55337400-55347800	Weak transcription	HSMMtube	muscle
32	chr14:55337600-55338000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:55337600-55338000	Weak transcription	Dnd41	blood
34	chr14:55337600-55346400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr14:55337600-55348600	Weak transcription	Hela-S3	cervix
36	chr14:55337800-55338000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:55337800-55338000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr14:55337800-55338000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr14:55337800-55338000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr14:55337800-55338000	Enhancers	Adipose Nuclei	Adipose
41	chr14:55337800-55338000	Enhancers	Liver	Liver
42	chr14:55337800-55338000	Enhancers	Left Ventricle	heart
43	chr14:55337800-55341600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr14:55337800-55345600	Weak transcription	Primary T cells fromperipheralblood	blood

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