Variant report

Variant	rs12459851
Chromosome Location	chr19:45668653-45668654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45646729..45650244-chr19:45666195..45669472,3	MCF-7	breast:
2	chr19:45664293..45670548-chr19:45677917..45684715,10	MCF-7	breast:
3	chr19:45663965..45672033-chr19:45672145..45675901,9	K562	blood:
4	chr19:45579089..45581981-chr19:45667540..45670366,2	K562	blood:
5	chr19:45667124..45670268-chr19:45680467..45683235,3	K562	blood:
6	chr19:45667869..45670716-chr19:45675537..45677306,2	MCF-7	breast:
7	chr19:45664074..45668689-chr19:45680998..45684242,7	MCF-7	breast:
8	chr19:45558584..45560889-chr19:45665988..45668898,2	K562	blood:
9	chr19:45665641..45668911-chr19:45670300..45671967,3	K562	blood:
10	chr19:45665456..45669944-chr19:45672662..45676859,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267545	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000170684	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10420443	1.00[AMR][1000 genomes]
rs10425380	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs12459817	1.00[ASW][hapmap];0.81[MKK][hapmap]
rs12460007	1.00[AMR][1000 genomes]
rs12460771	1.00[AMR][1000 genomes]
rs12461733	1.00[ASW][hapmap];0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1798099	chr19:45664218-45681988	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12459851	EML2	cis	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45660200-45674000	Weak transcription	A549	lung
2	chr19:45662800-45669000	Enhancers	Esophagus	oesophagus
3	chr19:45664000-45670200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:45665400-45669800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:45665400-45670000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:45665400-45670200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:45665400-45680400	Weak transcription	Brain Substantia Nigra	brain
8	chr19:45665400-45680600	Weak transcription	Fetal Lung	lung
9	chr19:45665600-45680400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:45665800-45674600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:45665800-45680200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:45665800-45680400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:45666000-45669200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr19:45666000-45669200	Enhancers	HMEC	breast
15	chr19:45666000-45669800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr19:45666200-45668800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr19:45666400-45670400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr19:45666600-45669000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr19:45666600-45671000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr19:45666800-45668800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr19:45667000-45669000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:45667000-45669000	Enhancers	Right Ventricle	heart
23	chr19:45667000-45669200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:45667000-45669200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:45667000-45670400	Enhancers	Fetal Thymus	thymus
26	chr19:45667000-45670600	Enhancers	Placenta	Placenta
27	chr19:45667200-45668800	Enhancers	Primary hematopoietic stem cells	blood
28	chr19:45667200-45668800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:45667200-45668800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:45667200-45669200	Enhancers	Primary B cells from peripheral blood	blood
31	chr19:45667400-45669000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:45667400-45669200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr19:45667400-45669400	Enhancers	Primary B cells from cord blood	blood
34	chr19:45667400-45681000	Weak transcription	Aorta	Aorta
35	chr19:45667600-45669200	Enhancers	Left Ventricle	heart
36	chr19:45667600-45672000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr19:45667800-45669800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr19:45667800-45669800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:45668000-45668800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:45668000-45669000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:45668000-45669800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr19:45668000-45670000	Weak transcription	HUVEC	blood vessel
43	chr19:45668000-45671000	Weak transcription	Hela-S3	cervix
44	chr19:45668000-45674600	Weak transcription	HSMMtube	muscle
45	chr19:45668000-45680600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr19:45668200-45669000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:45668200-45669800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr19:45668200-45669800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:45668200-45669800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr19:45668200-45670600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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