Variant report

Variant	rs12878653
Chromosome Location	chr14:64403004-64403005
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64402738..64405329-chr14:64411303..64414012,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10149728	0.95[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs10498512	0.82[EUR][1000 genomes]
rs10873172	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11623650	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1255856	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1255857	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1255867	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1255869	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1255872	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1255873	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1255874	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1255875	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1255876	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1255877	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1255878	0.84[EUR][1000 genomes]
rs1255879	0.84[EUR][1000 genomes]
rs1255880	0.84[EUR][1000 genomes]
rs1255881	0.80[EUR][1000 genomes]
rs1255883	0.84[EUR][1000 genomes]
rs1255885	0.84[EUR][1000 genomes]
rs1255887	0.84[EUR][1000 genomes]
rs1255890	0.83[EUR][1000 genomes]
rs1255891	0.83[EUR][1000 genomes]
rs1255892	0.83[EUR][1000 genomes]
rs1255896	0.83[EUR][1000 genomes]
rs1255900	0.82[EUR][1000 genomes]
rs1255901	0.82[EUR][1000 genomes]
rs1255902	0.82[EUR][1000 genomes]
rs1255903	0.80[EUR][1000 genomes]
rs1255905	0.82[EUR][1000 genomes]
rs1255908	0.83[EUR][1000 genomes]
rs1262235	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1262237	0.83[EUR][1000 genomes]
rs1266870	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1270051	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1270526	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1271567	0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[EUR][1000 genomes]
rs1272156	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs1272714	0.81[AMR][1000 genomes]
rs1273192	0.84[EUR][1000 genomes]
rs12881652	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1953241	0.85[ASW][hapmap];0.82[GIH][hapmap];0.83[LWK][hapmap]
rs2150291	0.83[LWK][hapmap]
rs2184292	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357175	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357176	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2792201	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28483877	0.82[EUR][1000 genomes]
rs2884111	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2994421	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2994422	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35224808	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61984073	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7156570	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8009321	0.82[EUR][1000 genomes]
rs9323442	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9323443	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs945027	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs945028	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12878653	SYNE2	cis	cerebellum	SCAN
rs12878653	DAAM1	cis	cerebellum	SCAN
rs12878653	C14orf39	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
2	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
3	chr14:64376000-64416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr14:64378000-64404800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr14:64378000-64416200	Weak transcription	Fetal Lung	lung
6	chr14:64378400-64416000	Weak transcription	Primary B cells from cord blood	blood
7	chr14:64379800-64409000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr14:64386400-64403800	Weak transcription	Esophagus	oesophagus
9	chr14:64386400-64405600	Weak transcription	Pancreas	Pancrea
10	chr14:64386600-64403400	Weak transcription	Gastric	stomach
11	chr14:64387000-64404200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr14:64387000-64416400	Weak transcription	Aorta	Aorta
13	chr14:64390200-64416400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr14:64390600-64418800	Weak transcription	HepG2	liver
15	chr14:64390800-64404000	Weak transcription	Placenta	Placenta
16	chr14:64390800-64408600	Weak transcription	Fetal Intestine Large	intestine
17	chr14:64392000-64405600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr14:64392000-64409000	Weak transcription	Fetal Intestine Small	intestine
19	chr14:64393200-64419800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:64393800-64403200	Weak transcription	Spleen	Spleen
21	chr14:64393800-64414800	Weak transcription	Fetal Muscle Leg	muscle
22	chr14:64394200-64403400	Weak transcription	Right Ventricle	heart
23	chr14:64395000-64403200	Weak transcription	Left Ventricle	heart
24	chr14:64395000-64491000	Weak transcription	Psoas Muscle	Psoas
25	chr14:64395600-64408000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr14:64396000-64405000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr14:64396000-64408400	Weak transcription	Fetal Kidney	kidney
28	chr14:64396000-64418600	Weak transcription	Fetal Heart	heart
29	chr14:64396800-64407200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:64397000-64403200	Weak transcription	Dnd41	blood
31	chr14:64397400-64409000	Weak transcription	Fetal Stomach	stomach
32	chr14:64400000-64409000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr14:64400000-64416400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr14:64400000-64419800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr14:64400200-64403200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr14:64400200-64405000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr14:64400200-64407200	Weak transcription	Liver	Liver
38	chr14:64400400-64403600	Weak transcription	Primary T cells from cord blood	blood
39	chr14:64400400-64404600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr14:64400400-64408000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr14:64400400-64409600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr14:64400600-64407800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr14:64400800-64403600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr14:64400800-64404000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr14:64400800-64404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr14:64400800-64404200	Weak transcription	HMEC	breast
47	chr14:64400800-64407800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr14:64400800-64417800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr14:64401000-64408400	Weak transcription	Brain Germinal Matrix	brain
50	chr14:64401000-64416200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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