Variant report

Variant	rs17115692
Chromosome Location	chr14:45395275-45395276
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:45387612..45390457-chr14:45393644..45395655,2	K562	blood:
2	chr14:45366158..45368654-chr14:45393073..45395433,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C14orf28-2	chr14:45394925-45395793	l_978_chr14:45283074-45311409_kidney

Variant related genes	Relation type
ENSG00000258633	Chromatin interaction
ENSG00000179476	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11846502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17115680	1.00[ASN][1000 genomes]
rs17115690	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[YRI][hapmap]
rs56803309	0.81[AFR][1000 genomes]
rs57261684	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57489965	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58557583	1.00[ASN][1000 genomes]
rs73334118	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73334121	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74046533	0.81[AFR][1000 genomes]
rs74046535	0.83[AFR][1000 genomes]
rs74046536	0.83[AMR][1000 genomes]
rs8016080	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]

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	nsv869289	chr14:44752382-45447415	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv901832	chr14:44847444-45415597	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1047886	chr14:45189653-45543182	Strong transcription Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv542079	chr14:45189653-45543182	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv901841	chr14:45198196-45719643	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1053437	chr14:45232269-45424222	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv1795667	chr14:45361680-45721052	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	esv1794986	chr14:45368685-45650813	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17115692	C14orf28	cis	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45368200-45397400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr14:45375400-45403000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:45382000-45400600	Weak transcription	Left Ventricle	heart
4	chr14:45382000-45408000	Weak transcription	Pancreas	Pancrea
5	chr14:45383000-45397600	Weak transcription	Liver	Liver
6	chr14:45383000-45405800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:45384400-45406800	Weak transcription	Fetal Muscle Leg	muscle
8	chr14:45384800-45397000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr14:45384800-45397400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr14:45384800-45408000	Weak transcription	Brain Hippocampus Middle	brain
11	chr14:45386600-45405600	Weak transcription	Fetal Lung	lung
12	chr14:45386800-45405600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr14:45388400-45398000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:45389600-45406800	Weak transcription	HSMMtube	muscle
15	chr14:45390000-45397400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr14:45390200-45398200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr14:45390200-45406800	Weak transcription	Fetal Stomach	stomach
18	chr14:45390400-45400600	Weak transcription	Primary T cells from cord blood	blood
19	chr14:45390400-45406600	Weak transcription	Brain Germinal Matrix	brain
20	chr14:45390400-45408200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr14:45390600-45397600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr14:45390600-45408400	Weak transcription	Fetal Brain Female	brain
23	chr14:45391200-45397000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:45391200-45400000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:45391200-45405800	Weak transcription	Fetal Intestine Large	intestine
26	chr14:45391200-45411000	Weak transcription	HSMM	muscle
27	chr14:45391200-45413000	Weak transcription	HUVEC	blood vessel
28	chr14:45391400-45406400	Weak transcription	Fetal Intestine Small	intestine
29	chr14:45391400-45406800	Weak transcription	Thymus	Thymus
30	chr14:45392200-45397400	Weak transcription	Adipose Nuclei	Adipose
31	chr14:45392400-45397400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr14:45392800-45396800	Weak transcription	Primary B cells from cord blood	blood
33	chr14:45393000-45397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr14:45393200-45396800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr14:45394200-45395600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr14:45394200-45413800	Weak transcription	HepG2	liver
37	chr14:45394400-45396200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr14:45394400-45397600	Weak transcription	NHDF-Ad	bronchial
39	chr14:45394400-45408000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr14:45394600-45408000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr14:45394800-45396800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr14:45394800-45406800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr14:45395000-45396800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr14:45395000-45397000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr14:45395000-45408000	Weak transcription	Gastric	stomach
46	chr14:45395200-45395400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr14:45395200-45395600	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr14:45395200-45397000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr14:45395200-45397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr14:45395200-45397600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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