Variant report

Variant	rs11158518
Chromosome Location	chr14:64350954-64350955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64350604..64352187-chr14:64354098..64356730,2	MCF-7	breast:
2	chr14:64350600..64353514-chr7:30543619..30546570,2	MCF-7	breast:
3	chr14:64349303..64352052-chr2:9373051..9375606,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006625	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11158515	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11626911	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11628650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12161903	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12431956	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12432760	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12435958	0.87[CHB][hapmap]
rs12586461	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590842	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17750888	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17750906	0.83[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	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4902253	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56376318	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60305436	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61985726	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61985748	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6573535	0.87[CHB][hapmap]
rs66460676	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66764453	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67011590	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67106029	0.91[ASN][1000 genomes]
rs67975797	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7140278	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143794	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7145302	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs7145736	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7146469	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7149405	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73276854	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8008800	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8010312	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs8010385	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8013611	0.91[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8016321	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8017009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951249	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951250	0.87[CHB][hapmap]
rs998242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[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
rs11158518	C14orf39	cis	cerebellum	SCAN
rs11158518	SYNE2	cis	cerebellum	SCAN
rs11158518	FLJ43390	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	chr14:64338000-64353800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:64338000-64355200	Weak transcription	Primary B cells from cord blood	blood
11	chr14:64339400-64366800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr14:64341000-64356400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr14:64341000-64357200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:64341200-64351000	Weak transcription	Right Ventricle	heart
15	chr14:64341200-64352200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:64341200-64352400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:64341200-64354000	Weak transcription	Dnd41	blood
18	chr14:64341200-64354800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr14:64341200-64356400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr14:64341200-64356400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr14:64341200-64356600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr14:64341200-64357000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:64341200-64357200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr14:64341200-64357200	Weak transcription	Fetal Lung	lung
25	chr14:64341200-64357200	Weak transcription	Fetal Muscle Leg	muscle
26	chr14:64341400-64352400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr14:64341400-64352600	Weak transcription	Stomach Mucosa	stomach
28	chr14:64341400-64356600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr14:64341400-64356600	Weak transcription	Fetal Kidney	kidney
30	chr14:64341400-64366800	Weak transcription	Primary T cells from cord blood	blood
31	chr14:64342400-64354800	Weak transcription	Aorta	Aorta
32	chr14:64342400-64357200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:64342600-64352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr14:64342600-64352400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr14:64342600-64357400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr14:64342800-64351000	Weak transcription	Lung	lung
37	chr14:64342800-64351600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr14:64342800-64352400	Weak transcription	Adipose Nuclei	Adipose
39	chr14:64342800-64354200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr14:64342800-64357000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr14:64342800-64357200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr14:64342800-64360400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr14:64342800-64360400	Weak transcription	Hela-S3	cervix
44	chr14:64342800-64368400	Weak transcription	Esophagus	oesophagus
45	chr14:64343600-64359400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr14:64344000-64351000	Weak transcription	NHEK	skin
47	chr14:64344000-64357200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr14:64344000-64357200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:64344200-64352000	Weak transcription	Brain Germinal Matrix	brain
50	chr14:64344400-64351200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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