Variant report

Variant	rs1713418
Chromosome Location	chr14:20834809-20834810
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	chr14:20832744..20836299-chr14:20840104..20843519,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129566	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10134743	0.82[TSI][hapmap]
rs1132644	0.83[MEX][hapmap]
rs11623837	0.82[TSI][hapmap]
rs12889262	0.83[MEX][hapmap]
rs1713419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784244	0.83[MEX][hapmap]
rs6575164	0.84[MEX][hapmap];0.83[TSI][hapmap]
rs7160770	0.88[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers 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	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
4	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
5	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription 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	71 gene(s)	inside rSNPs	diseases
6	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	esv21015	chr14:20800765-21257878	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1713418	PARP2	cis	parietal	SCAN
rs1713418	RPPH1	cis	cerebellum	SCAN
rs1713418	PARP2	cis	cerebellum	SCAN
rs1713418	OR4K1	cis	cerebellum	SCAN
rs1713418	CCNB1IP1	cis	parietal	SCAN
rs1713418	CCNB1IP1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20812400-20880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:20812600-20841000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr14:20812600-20845600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:20813200-20869200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr14:20824600-20840800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:20824800-20836000	Weak transcription	Psoas Muscle	Psoas
7	chr14:20824800-20836200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr14:20824800-20839200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:20825000-20836600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr14:20825000-20836800	Weak transcription	Stomach Mucosa	stomach
11	chr14:20825200-20863200	Weak transcription	Fetal Heart	heart
12	chr14:20825800-20837400	Weak transcription	Fetal Kidney	kidney
13	chr14:20825800-20846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:20826000-20836000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:20826200-20839000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr14:20826200-20841400	Weak transcription	K562	blood
17	chr14:20826400-20836600	Weak transcription	Brain Substantia Nigra	brain
18	chr14:20826400-20836800	Weak transcription	Brain Angular Gyrus	brain
19	chr14:20826400-20847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:20826600-20836000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:20826600-20836200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr14:20826600-20840800	Weak transcription	Fetal Brain Male	brain
23	chr14:20826800-20836000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr14:20827200-20836400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:20827400-20835600	Weak transcription	Fetal Brain Female	brain
26	chr14:20827600-20836000	Weak transcription	A549	lung
27	chr14:20827800-20836000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr14:20827800-20836800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr14:20827800-20840400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr14:20828000-20836000	Weak transcription	HepG2	liver
31	chr14:20828000-20836600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr14:20828000-20842600	Strong transcription	Fetal Intestine Small	intestine
33	chr14:20828200-20836000	Weak transcription	Brain Germinal Matrix	brain
34	chr14:20829000-20836000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr14:20829000-20855800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr14:20829200-20877000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr14:20829400-20843400	Strong transcription	Fetal Intestine Large	intestine
38	chr14:20829400-20855800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr14:20829400-20876800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr14:20829600-20876800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr14:20829800-20864800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr14:20829800-20877400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr14:20830400-20869000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:20830400-20876800	Strong transcription	Fetal Stomach	stomach
45	chr14:20830400-20877200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr14:20831000-20860800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr14:20831000-20860800	Strong transcription	Primary T cells from cord blood	blood
48	chr14:20831000-20868200	Strong transcription	Placenta	Placenta
49	chr14:20831200-20842400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr14:20831200-20844200	Strong transcription	Rectal Mucosa Donor 29	rectum

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