Variant report

Variant	rs8005899
Chromosome Location	chr14:64354419-64354420
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	chr14:64350604..64352187-chr14:64354098..64356730,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11158512	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11158516	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11847056	0.81[ASN][1000 genomes]
rs11850357	0.81[ASN][1000 genomes]
rs12435958	0.85[MEX][hapmap];0.89[YRI][hapmap]
rs12586475	0.80[ASN][1000 genomes]
rs12587472	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12588087	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12589129	0.80[ASN][1000 genomes]
rs12589296	0.80[ASN][1000 genomes]
rs12878017	0.80[ASN][1000 genomes]
rs12886839	0.81[ASN][1000 genomes]
rs12894053	0.95[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12894864	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1959034	0.96[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1959035	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2149677	0.81[ASN][1000 genomes]
rs2150291	0.86[JPT][hapmap]
rs2210650	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2275018	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2356996	0.81[ASN][1000 genomes]
rs2357001	0.90[MEX][hapmap];0.89[YRI][hapmap]
rs2357002	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2357003	0.87[CEU][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34780876	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4243627	0.80[ASN][1000 genomes]
rs4902247	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4902248	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6573534	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7143343	0.81[ASN][1000 genomes]
rs7143535	0.80[ASN][1000 genomes]
rs7145302	0.81[CHB][hapmap];0.90[MEX][hapmap]
rs7145657	0.86[ASN][1000 genomes]
rs7146821	0.96[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7148088	0.80[ASN][1000 genomes]
rs7149766	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7153101	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7155129	0.81[ASN][1000 genomes]
rs7157314	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7157323	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7158974	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7160127	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7493416	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7493843	0.81[ASN][1000 genomes]
rs8008552	0.81[ASN][1000 genomes]
rs8015158	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8015311	0.81[ASN][1000 genomes]
rs8015354	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8022917	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs945030	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs954730	0.96[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9707224	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs998241	0.96[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv564904	chr14:64346190-64416898	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1793389	chr14:64346190-64457224	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8005899	FLJ43390	cis	cerebellum	SCAN
rs8005899	SYNE2	cis	parietal	SCAN
rs8005899	SYT16	cis	parietal	SCAN
rs8005899	SYNE2	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr14:64327600-64360000	Weak transcription	Gastric	stomach
3	chr14:64331200-64356400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr14:64335200-64360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:64336800-64362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr14:64337000-64357200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr14:64337000-64365200	Weak transcription	Fetal Thymus	thymus
8	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
9	chr14:64338000-64355200	Weak transcription	Primary B cells from cord blood	blood
10	chr14:64339400-64366800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr14:64341000-64356400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr14:64341000-64357200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:64341200-64354800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr14:64341200-64356400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr14:64341200-64356400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr14:64341200-64356600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:64341200-64357000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:64341200-64357200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr14:64341200-64357200	Weak transcription	Fetal Lung	lung
20	chr14:64341200-64357200	Weak transcription	Fetal Muscle Leg	muscle
21	chr14:64341400-64356600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr14:64341400-64356600	Weak transcription	Fetal Kidney	kidney
23	chr14:64341400-64366800	Weak transcription	Primary T cells from cord blood	blood
24	chr14:64342400-64354800	Weak transcription	Aorta	Aorta
25	chr14:64342400-64357200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr14:64342600-64357400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr14:64342800-64357000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr14:64342800-64357200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:64342800-64360400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr14:64342800-64360400	Weak transcription	Hela-S3	cervix
31	chr14:64342800-64368400	Weak transcription	Esophagus	oesophagus
32	chr14:64343600-64359400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr14:64344000-64357200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:64344000-64357200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr14:64344400-64356600	Weak transcription	GM12878-XiMat	blood
36	chr14:64344400-64357000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr14:64344400-64357400	Weak transcription	Fetal Intestine Large	intestine
38	chr14:64344600-64357200	Weak transcription	HMEC	breast
39	chr14:64344800-64357200	Weak transcription	Small Intestine	intestine
40	chr14:64345000-64356800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr14:64345000-64357200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr14:64345000-64357200	Weak transcription	Ovary	ovary
43	chr14:64345000-64357200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr14:64345200-64354600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr14:64345200-64357200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr14:64345800-64357200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr14:64346600-64357200	Weak transcription	Fetal Brain Female	brain
48	chr14:64348800-64356400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr14:64349400-64357600	Weak transcription	Placenta	Placenta
50	chr14:64349400-64366600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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