Variant report

Variant	rs17739146
Chromosome Location	chr14:55308004-55308005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55305231..55308673-chr14:55367563..55370969,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131979	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10151058	1.00[ASN][1000 genomes]
rs11845908	1.00[ASN][1000 genomes]
rs11845954	1.00[ASN][1000 genomes]
rs11847254	1.00[ASN][1000 genomes]
rs1354	1.00[ASN][1000 genomes]
rs17128008	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17253584	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17253591	0.85[CEU][hapmap]
rs17671005	0.85[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs17671485	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738863	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17738966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951437	1.00[ASN][1000 genomes]
rs1951438	1.00[ASN][1000 genomes]
rs2004633	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28678578	1.00[ASN][1000 genomes]
rs41298434	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4340245	1.00[ASN][1000 genomes]
rs45454691	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55934565	1.00[ASN][1000 genomes]
rs56924179	0.94[EUR][1000 genomes]
rs61744409	1.00[ASN][1000 genomes]
rs7141175	0.84[CEU][hapmap]
rs7147147	1.00[ASN][1000 genomes]
rs7148831	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73278735	1.00[ASN][1000 genomes]
rs73278772	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7493025	0.99[EUR][1000 genomes]
rs8016944	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17739146	LANCL3	trans	lymphoblastoid	RTeQTL
rs17739146	PYGL	cis	cerebellum	SCAN
rs17739146	TBPL2	cis	parietal	SCAN
rs17739146	EXOC5	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55299200-55308200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:55301000-55310000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr14:55303400-55337000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:55304800-55309200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr14:55305000-55320400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr14:55305200-55312200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr14:55305200-55337200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr14:55305400-55314000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr14:55305400-55325800	Weak transcription	Spleen	Spleen
10	chr14:55305600-55313200	Strong transcription	Primary T cells from cord blood	blood
11	chr14:55305800-55308800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr14:55305800-55313000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr14:55305800-55313200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:55305800-55313600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr14:55305800-55321000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr14:55305800-55326400	Weak transcription	Fetal Thymus	thymus
17	chr14:55306000-55308600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr14:55306000-55308600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr14:55306000-55309000	Weak transcription	Right Ventricle	heart
20	chr14:55306000-55314200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr14:55306200-55309400	Enhancers	Liver	Liver
22	chr14:55306200-55320800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr14:55306200-55337000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr14:55306400-55309800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr14:55306400-55311200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr14:55306400-55311400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr14:55306400-55312800	Weak transcription	Gastric	stomach
28	chr14:55306400-55336800	Weak transcription	Dnd41	blood
29	chr14:55306600-55308200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:55306600-55321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr14:55306600-55336600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr14:55306800-55309200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr14:55306800-55327400	Weak transcription	Pancreas	Pancrea
34	chr14:55306800-55337000	Weak transcription	Brain Anterior Caudate	brain
35	chr14:55307000-55310200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr14:55307000-55312400	Weak transcription	Stomach Mucosa	stomach
37	chr14:55307000-55313400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr14:55307200-55308200	Weak transcription	Adipose Nuclei	Adipose
39	chr14:55307200-55308200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr14:55307200-55308200	Strong transcription	Fetal Intestine Large	intestine
41	chr14:55307200-55308200	Strong transcription	Left Ventricle	heart
42	chr14:55307200-55308200	Enhancers	HepG2	liver
43	chr14:55307200-55308600	Strong transcription	Fetal Intestine Small	intestine
44	chr14:55307200-55309800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:55307200-55309800	Strong transcription	GM12878-XiMat	blood
46	chr14:55307200-55313000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr14:55307400-55309600	Weak transcription	Aorta	Aorta
48	chr14:55307400-55309800	Weak transcription	Fetal Muscle Leg	muscle
49	chr14:55307400-55309800	Weak transcription	Fetal Stomach	stomach
50	chr14:55307400-55310200	Strong transcription	Primary B cells from peripheral blood	blood

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