Variant report

Variant	rs1953241
Chromosome Location	chr14:64374254-64374255
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	chr14:64372158..64375131-chr14:64377283..64378855,2	MCF-7	breast:
2	chr14:64373323..64375325-chr14:64805642..64807746,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10873172	0.82[GIH][hapmap]
rs12894053	0.90[JPT][hapmap]
rs1959034	0.90[JPT][hapmap]
rs2150291	0.92[ASW][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2357003	0.82[CEU][hapmap];0.85[GIH][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1953241	SYNE2	cis	cerebellum	SCAN
rs1953241	ADORA3	trans	parietal	SCAN
rs1953241	SYNE2	cis	parietal	SCAN
rs1953241	FLJ43390	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
2	chr14:64358200-64375800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:64358200-64377600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:64358800-64377600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr14:64360600-64382200	Weak transcription	Psoas Muscle	Psoas
6	chr14:64360800-64377800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr14:64363400-64374400	Weak transcription	Fetal Intestine Small	intestine
8	chr14:64363400-64375200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:64363400-64375400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr14:64363800-64375400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr14:64364400-64385200	Weak transcription	Pancreas	Pancrea
12	chr14:64364600-64375400	Weak transcription	Aorta	Aorta
13	chr14:64364600-64387800	Weak transcription	HMEC	breast
14	chr14:64364800-64375400	Weak transcription	Hela-S3	cervix
15	chr14:64365000-64375000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr14:64365000-64375000	Weak transcription	Fetal Kidney	kidney
17	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
18	chr14:64365200-64375800	Weak transcription	Fetal Stomach	stomach
19	chr14:64365200-64386200	Weak transcription	Gastric	stomach
20	chr14:64365400-64376600	Weak transcription	Placenta	Placenta
21	chr14:64365400-64379800	Weak transcription	Fetal Thymus	thymus
22	chr14:64365400-64393600	Weak transcription	Right Ventricle	heart
23	chr14:64365600-64375400	Weak transcription	Stomach Mucosa	stomach
24	chr14:64367400-64375200	Weak transcription	Right Atrium	heart
25	chr14:64367400-64375400	Weak transcription	Left Ventricle	heart
26	chr14:64367400-64378000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr14:64367800-64377400	Weak transcription	Primary B cells from cord blood	blood
28	chr14:64368600-64375400	Weak transcription	Dnd41	blood
29	chr14:64368600-64375400	Weak transcription	Osteobl	bone
30	chr14:64369400-64375400	Weak transcription	Adipose Nuclei	Adipose
31	chr14:64369600-64375000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr14:64369600-64375200	Weak transcription	Ovary	ovary
33	chr14:64369600-64375400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr14:64369600-64377600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:64369800-64374400	Weak transcription	Small Intestine	intestine
36	chr14:64369800-64374800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:64369800-64376200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr14:64369800-64376400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr14:64369800-64386200	Weak transcription	Esophagus	oesophagus
40	chr14:64370800-64375400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr14:64372000-64374600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr14:64372200-64378000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr14:64373000-64376000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr14:64373200-64376400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr14:64373400-64375200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr14:64373600-64374800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr14:64373600-64375200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr14:64373600-64375200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr14:64373600-64375400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr14:64373600-64376000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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