Variant report

Variant	rs10142318
Chromosome Location	chr14:64604281-64604282
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	SMC3	chr14:64604256-64604939	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr14:64604262-64604850	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr14:64604279-64604839	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:64604081..64605250-chr14:64769694..64771281,8	MCF-7	breast:
2	chr14:64604106..64605326-chr14:64769895..64770529,5	MCF-7	breast:
3	chr14:64604050..64605326-chr14:64761261..64762254,11	MCF-7	breast:
4	chr14:64603180..64606087-chr14:64758576..64761185,2	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region
ENSG00000140009	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10047814	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10047815	0.85[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap]
rs10047901	0.94[ASN][1000 genomes]
rs10136099	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10136662	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137370	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10137426	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10137665	0.90[ASN][1000 genomes]
rs10142480	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10151446	0.88[ASN][1000 genomes]
rs11158531	0.99[ASN][1000 genomes]
rs11158532	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11849394	0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12147438	1.00[ASN][1000 genomes]
rs12587140	0.84[ASN][1000 genomes]
rs12587924	0.90[ASN][1000 genomes]
rs12590062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12590378	0.85[CHB][hapmap]
rs2184288	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34994562	0.93[ASN][1000 genomes]
rs45472593	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57018718	0.94[ASN][1000 genomes]
rs7140578	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7158393	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7159213	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7160091	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7161361	0.93[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8003196	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8021831	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8022222	0.86[EUR][1000 genomes]
rs8023139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9323446	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv564906	chr14:64595673-64612858	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10142318	PPM1A	cis	parietal	SCAN
rs10142318	SNAPC1	cis	parietal	SCAN
rs10142318	FNTB	cis	parietal	SCAN
rs10142318	FLJ43390	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64544000-64616200	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr14:64567200-64616200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr14:64567400-64647200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr14:64577800-64616200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr14:64578200-64649000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr14:64578600-64649000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:64579600-64611000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr14:64581400-64613400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:64581800-64650400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr14:64583400-64649000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr14:64583600-64605400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr14:64583600-64611800	Strong transcription	Dnd41	blood
13	chr14:64583600-64638000	Strong transcription	Placenta	Placenta
14	chr14:64584400-64616000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr14:64584600-64607000	Weak transcription	HUVEC	blood vessel
16	chr14:64584600-64623000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:64584800-64605400	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr14:64585400-64613400	Weak transcription	HSMM	muscle
19	chr14:64585600-64607400	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr14:64585600-64615600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr14:64585800-64614400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr14:64586000-64649000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr14:64586400-64631800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr14:64586600-64614000	Weak transcription	Fetal Heart	heart
25	chr14:64588800-64611600	Strong transcription	Primary T cells from cord blood	blood
26	chr14:64590200-64634000	Weak transcription	HepG2	liver
27	chr14:64590400-64608800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr14:64591000-64649000	Strong transcription	Liver	Liver
29	chr14:64592000-64604400	Strong transcription	Fetal Lung	lung
30	chr14:64592600-64608200	Weak transcription	Hela-S3	cervix
31	chr14:64592800-64608600	Weak transcription	Fetal Brain Male	brain
32	chr14:64593600-64608600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr14:64593600-64609000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:64593600-64615800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr14:64593800-64608600	Weak transcription	Small Intestine	intestine
36	chr14:64593800-64608800	Weak transcription	Colon Smooth Muscle	Colon
37	chr14:64593800-64613400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr14:64594200-64605600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr14:64594600-64609200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr14:64594600-64653200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr14:64594800-64619600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr14:64595200-64605000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr14:64595600-64607400	Strong transcription	Fetal Stomach	stomach
44	chr14:64596400-64653000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr14:64597000-64608400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr14:64597000-64608800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr14:64597000-64609000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr14:64597000-64609200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr14:64597000-64626400	Weak transcription	Psoas Muscle	Psoas
50	chr14:64597200-64608200	Weak transcription	Primary B cells from peripheral blood	blood

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