Variant report

Variant	rs1713430
Chromosome Location	chr14:20815013-20815014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr14:20814908-20815221	HepG2	liver:	n/a	n/a
2	JUN	chr14:20814923-20815199	HepG2	liver:	n/a	chr14:20815049-20815062

No.	Distal block	Cell Line	Cell type
1	chr14:20808270..20815666-chr14:20919802..20926735,19	MCF-7	breast:
2	chr14:20814045..20815717-chr14:20936287..20939086,2	K562	blood:
3	chr14:20811638..20813233-chr14:20813576..20815950,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNB1IP1-2	chr14:20814724-20815047	ENSG00000254846.1

Variant related genes	Relation type
PARP2	TF binding region
RPPH1	TF binding region
ENSG00000092094	Chromatin interaction
ENSG00000198805	Chromatin interaction
ENSG00000129484	Chromatin interaction
ENSG00000259001	Chromatin interaction
ENSG00000100823	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11623831	0.83[CHB][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs1713411	0.88[YRI][hapmap]
rs1713413	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1713414	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1713415	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1760912	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1760918	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1760919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1760921	0.90[YRI][hapmap]
rs1760923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889363	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs1953224	0.93[EUR][1000 genomes]
rs2297617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319190	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2678682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2678683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28410239	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28436942	0.87[EUR][1000 genomes]
rs3093870	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3093900	0.83[EUR][1000 genomes]
rs3093907	0.84[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs3093909	0.83[EUR][1000 genomes]
rs4981975	0.82[AFR][1000 genomes]
rs6575168	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs7159947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7160770	0.85[ASW][hapmap];0.80[MEX][hapmap];0.82[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	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	nsv1042025	chr14:20787961-20817851	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
8	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1713430	PARP2	cis	parietal	SCAN
rs1713430	TTC5	cis	cerebellum	SCAN
rs1713430	CCNB1IP1	cis	cerebellum	SCAN
rs1713430	PARP2	cis	cerebellum	SCAN
rs1713430	PRMT5	cis	parietal	SCAN
rs1713430	CCNB1IP1	cis	parietal	SCAN
rs1713430	RPPH1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20812000-20820600	Weak transcription	Spleen	Spleen
2	chr14:20812000-20822600	Weak transcription	Gastric	stomach
3	chr14:20812200-20815200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:20812200-20815200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:20812200-20815800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr14:20812200-20817800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr14:20812200-20822600	Weak transcription	Pancreas	Pancrea
8	chr14:20812200-20824000	Weak transcription	Aorta	Aorta
9	chr14:20812200-20825400	Weak transcription	Esophagus	oesophagus
10	chr14:20812400-20815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr14:20812400-20815200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr14:20812400-20815800	Weak transcription	Small Intestine	intestine
13	chr14:20812400-20816000	Weak transcription	Thymus	Thymus
14	chr14:20812400-20818000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr14:20812400-20820400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr14:20812400-20824400	Weak transcription	Stomach Mucosa	stomach
17	chr14:20812400-20880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr14:20812600-20815200	Weak transcription	Brain Substantia Nigra	brain
19	chr14:20812600-20815600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr14:20812600-20816000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr14:20812600-20816000	Weak transcription	Colon Smooth Muscle	Colon
22	chr14:20812600-20816600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr14:20812600-20817000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr14:20812600-20817200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:20812600-20817200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:20812600-20817200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:20812600-20817600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr14:20812600-20817800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr14:20812600-20817800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:20812600-20817800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr14:20812600-20818000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr14:20812600-20820200	Weak transcription	Colonic Mucosa	Colon
33	chr14:20812600-20820600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr14:20812600-20820600	Weak transcription	Psoas Muscle	Psoas
35	chr14:20812600-20820600	Weak transcription	Right Ventricle	heart
36	chr14:20812600-20820800	Weak transcription	NHDF-Ad	bronchial
37	chr14:20812600-20822200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr14:20812600-20824400	Weak transcription	Fetal Heart	heart
39	chr14:20812600-20831800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr14:20812600-20834600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr14:20812600-20841000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr14:20812600-20845600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr14:20812800-20815200	Weak transcription	Osteobl	bone
44	chr14:20812800-20818400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr14:20812800-20820600	Weak transcription	NHLF	lung
46	chr14:20812800-20824000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr14:20813000-20827000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr14:20813000-20827800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr14:20813000-20827800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr14:20813000-20830800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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