Variant report

Variant	rs17750888
Chromosome Location	chr14:64355420-64355421
allele	A/C
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: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11158515	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11158518	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626911	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11628650	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12161903	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12431956	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12432760	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12435958	0.87[CHB][hapmap]
rs12586461	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590842	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17750906	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1958413	0.85[JPT][hapmap]
rs2357001	0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[ASN][1000 genomes]
rs4899121	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4902253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56376318	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60305436	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61985726	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61985748	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6573535	0.87[CHB][hapmap]
rs66460676	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66764453	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67011590	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67106029	0.91[ASN][1000 genomes]
rs67975797	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7140278	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143794	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7145302	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs7145736	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7146469	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7149405	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73276854	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8008800	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8010312	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs8010385	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8013611	0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8016321	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8017009	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951249	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951250	0.87[CHB][hapmap]
rs998242	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17750888	SYNE2	cis	cerebellum	SCAN
rs17750888	FLJ43390	cis	cerebellum	SCAN
rs17750888	C14orf39	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64327600-64360000	Weak transcription	Gastric	stomach
2	chr14:64331200-64356400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr14:64335200-64360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:64336800-64362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:64337000-64357200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr14:64337000-64365200	Weak transcription	Fetal Thymus	thymus
7	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
8	chr14:64339400-64366800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr14:64341000-64356400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr14:64341000-64357200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr14:64341200-64356400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr14:64341200-64356400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr14:64341200-64356600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr14:64341200-64357000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr14:64341200-64357200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr14:64341200-64357200	Weak transcription	Fetal Lung	lung
17	chr14:64341200-64357200	Weak transcription	Fetal Muscle Leg	muscle
18	chr14:64341400-64356600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr14:64341400-64356600	Weak transcription	Fetal Kidney	kidney
20	chr14:64341400-64366800	Weak transcription	Primary T cells from cord blood	blood
21	chr14:64342400-64357200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr14:64342600-64357400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr14:64342800-64357000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:64342800-64357200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr14:64342800-64360400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr14:64342800-64360400	Weak transcription	Hela-S3	cervix
27	chr14:64342800-64368400	Weak transcription	Esophagus	oesophagus
28	chr14:64343600-64359400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr14:64344000-64357200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:64344000-64357200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:64344400-64356600	Weak transcription	GM12878-XiMat	blood
32	chr14:64344400-64357000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr14:64344400-64357400	Weak transcription	Fetal Intestine Large	intestine
34	chr14:64344600-64357200	Weak transcription	HMEC	breast
35	chr14:64344800-64357200	Weak transcription	Small Intestine	intestine
36	chr14:64345000-64356800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr14:64345000-64357200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr14:64345000-64357200	Weak transcription	Ovary	ovary
39	chr14:64345000-64357200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr14:64345200-64357200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr14:64345800-64357200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr14:64346600-64357200	Weak transcription	Fetal Brain Female	brain
43	chr14:64348800-64356400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr14:64349400-64357600	Weak transcription	Placenta	Placenta
45	chr14:64349400-64366600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr14:64349600-64357600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr14:64349600-64366000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr14:64351400-64357000	Weak transcription	NHEK	skin
49	chr14:64351400-64357200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr14:64351400-64357400	Weak transcription	Fetal Intestine Small	intestine

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