Variant report

Variant	rs1959034
Chromosome Location	chr14:64336479-64336480
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	chr14:64318570..64321307-chr14:64334480..64337114,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11158510	0.81[AFR][1000 genomes]
rs11158512	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11158516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11845009	0.82[AFR][1000 genomes]
rs11847056	0.80[ASN][1000 genomes]
rs11848677	0.84[AFR][1000 genomes]
rs11850357	0.80[ASN][1000 genomes]
rs12435958	0.85[MEX][hapmap]
rs12586475	0.81[AFR][1000 genomes]
rs12587472	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588087	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12589129	0.81[AFR][1000 genomes]
rs12589296	0.84[AFR][1000 genomes]
rs12878017	0.81[AFR][1000 genomes]
rs12886839	0.80[ASN][1000 genomes]
rs12890491	0.81[AFR][1000 genomes]
rs12892314	0.84[AFR][1000 genomes]
rs12894053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12894864	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1953241	0.90[JPT][hapmap]
rs1959035	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149677	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2150291	0.87[CHB][hapmap]
rs2210650	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275018	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2356996	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2357001	0.90[MEX][hapmap]
rs2357002	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2357003	0.91[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34780876	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4243627	0.81[AFR][1000 genomes]
rs4902247	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4902248	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6573534	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6573535	0.89[YRI][hapmap]
rs7143343	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7143535	0.84[AFR][1000 genomes]
rs7145302	0.84[ASW][hapmap];0.90[MEX][hapmap];0.90[YRI][hapmap]
rs7145657	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7146821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7148088	0.84[AFR][1000 genomes]
rs7148584	0.83[AFR][1000 genomes]
rs7149766	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7153101	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7155129	0.80[ASN][1000 genomes]
rs7157314	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7157323	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7158974	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7160127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7493416	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7493843	0.80[ASN][1000 genomes]
rs8005553	0.81[AFR][1000 genomes]
rs8005899	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8008552	0.80[ASN][1000 genomes]
rs8015158	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8015311	0.80[ASN][1000 genomes]
rs8015354	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8022917	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs945030	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951250	0.86[YRI][hapmap]
rs954730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9707224	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs998241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1959034	SYT16	cis	parietal	SCAN
rs1959034	SYNE2	cis	cerebellum	SCAN
rs1959034	SYNE2	cis	parietal	SCAN
rs1959034	FLJ43390	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64321200-64340600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:64321400-64350200	Weak transcription	Fetal Stomach	stomach
3	chr14:64322800-64340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:64322800-64340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:64323200-64340200	Weak transcription	Left Ventricle	heart
6	chr14:64323200-64340400	Weak transcription	Spleen	Spleen
7	chr14:64324600-64341400	Weak transcription	HSMM	muscle
8	chr14:64327200-64340600	Weak transcription	Right Ventricle	heart
9	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr14:64327600-64360000	Weak transcription	Gastric	stomach
11	chr14:64327800-64342200	Weak transcription	Esophagus	oesophagus
12	chr14:64330200-64343600	Weak transcription	Brain Germinal Matrix	brain
13	chr14:64330600-64338200	Enhancers	Primary B cells from peripheral blood	blood
14	chr14:64331200-64336600	Weak transcription	HMEC	breast
15	chr14:64331200-64356400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:64331400-64339800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr14:64331400-64340400	Weak transcription	Fetal Heart	heart
18	chr14:64331400-64340800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr14:64331400-64342200	Weak transcription	NHLF	lung
20	chr14:64331600-64336600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr14:64331600-64336600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr14:64331600-64336600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr14:64331600-64336600	Weak transcription	HUVEC	blood vessel
24	chr14:64331600-64336800	Weak transcription	Osteobl	bone
25	chr14:64331600-64340400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr14:64331600-64340400	Weak transcription	Right Atrium	heart
27	chr14:64331600-64340800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr14:64331600-64341000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr14:64331600-64341800	Weak transcription	NHDF-Ad	bronchial
30	chr14:64331800-64341400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr14:64332200-64336600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr14:64332200-64336600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr14:64332400-64338000	Enhancers	Primary B cells from cord blood	blood
34	chr14:64332600-64337200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr14:64333000-64341000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr14:64333200-64340400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr14:64333200-64340400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr14:64333400-64340400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr14:64333400-64340600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr14:64334400-64337000	Enhancers	Fetal Intestine Small	intestine
41	chr14:64334400-64337000	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr14:64334400-64337200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr14:64334600-64337000	Enhancers	Small Intestine	intestine
44	chr14:64335000-64337000	Enhancers	Liver	Liver
45	chr14:64335200-64336600	Weak transcription	Fetal Thymus	thymus
46	chr14:64335200-64340400	Weak transcription	Lung	lung
47	chr14:64335200-64340400	Weak transcription	Ovary	ovary
48	chr14:64335200-64341800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr14:64335200-64342200	Weak transcription	Placenta	Placenta
50	chr14:64335200-64342200	Weak transcription	Pancreas	Pancrea

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