Variant report

Variant	rs8016321
Chromosome Location	chr14:64340877-64340878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64332982..64334814-chr14:64338976..64341175,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11158515	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11158518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626911	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11628650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12161903	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12431956	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12432760	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12435958	0.87[CHB][hapmap]
rs12586461	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590842	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17750888	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17750906	0.94[ASN][1000 genomes]
rs1958413	0.85[JPT][hapmap]
rs2357001	0.87[CHB][hapmap];0.90[CHD][hapmap]
rs34486661	0.80[ASN][1000 genomes]
rs4899121	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902249	0.80[ASN][1000 genomes]
rs4902253	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56376318	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56401218	0.81[ASN][1000 genomes]
rs60305436	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61985718	0.80[ASN][1000 genomes]
rs61985726	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61985748	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6573535	0.87[CHB][hapmap]
rs66460676	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66764453	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67011590	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67106029	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67975797	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140278	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143794	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7145302	0.86[CHB][hapmap];0.92[CHD][hapmap];0.80[ASN][1000 genomes]
rs7145736	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7146469	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7149405	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7149609	0.80[ASN][1000 genomes]
rs73276854	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8008800	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8010312	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs8010385	0.93[ASN][1000 genomes]
rs8013611	0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8015374	0.80[ASN][1000 genomes]
rs8017009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951249	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951250	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs998242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8016321	C14orf39	cis	cerebellum	SCAN
rs8016321	SYNE2	cis	cerebellum	SCAN
rs8016321	FLJ43390	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64321400-64350200	Weak transcription	Fetal Stomach	stomach
2	chr14:64324600-64341400	Weak transcription	HSMM	muscle
3	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr14:64327600-64360000	Weak transcription	Gastric	stomach
5	chr14:64327800-64342200	Weak transcription	Esophagus	oesophagus
6	chr14:64330200-64343600	Weak transcription	Brain Germinal Matrix	brain
7	chr14:64331200-64356400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:64331400-64342200	Weak transcription	NHLF	lung
9	chr14:64331600-64341000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr14:64331600-64341800	Weak transcription	NHDF-Ad	bronchial
11	chr14:64331800-64341400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr14:64333000-64341000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:64335200-64341800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:64335200-64342200	Weak transcription	Placenta	Placenta
15	chr14:64335200-64342200	Weak transcription	Pancreas	Pancrea
16	chr14:64335200-64360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:64335800-64342000	Weak transcription	Colon Smooth Muscle	Colon
18	chr14:64336800-64341400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr14:64336800-64362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr14:64337000-64341000	Weak transcription	Small Intestine	intestine
21	chr14:64337000-64341800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr14:64337000-64342000	Weak transcription	Liver	Liver
23	chr14:64337000-64342000	Weak transcription	Osteobl	bone
24	chr14:64337000-64342200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr14:64337000-64342400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr14:64337000-64343600	Weak transcription	Fetal Intestine Large	intestine
27	chr14:64337000-64357200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr14:64337000-64365200	Weak transcription	Fetal Thymus	thymus
29	chr14:64337200-64341600	Weak transcription	HUVEC	blood vessel
30	chr14:64337600-64342600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr14:64337600-64343600	Weak transcription	A549	lung
32	chr14:64337800-64342000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
34	chr14:64338000-64353800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr14:64338000-64355200	Weak transcription	Primary B cells from cord blood	blood
36	chr14:64338600-64341200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:64339400-64366800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr14:64339800-64341200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr14:64339800-64341200	Enhancers	Dnd41	blood
40	chr14:64340000-64342400	Enhancers	HMEC	breast
41	chr14:64340000-64342800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr14:64340200-64341200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr14:64340200-64342200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr14:64340200-64342800	Enhancers	Adipose Nuclei	Adipose
45	chr14:64340200-64344000	Enhancers	Left Ventricle	heart
46	chr14:64340400-64341000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr14:64340400-64341000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr14:64340400-64341000	Flanking Active TSS	NHEK	skin
49	chr14:64340400-64341200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr14:64340400-64341200	Enhancers	HUES64 Cell Line	embryonic stem cell

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