Variant report

Variant	rs2150288
Chromosome Location	chr14:64377718-64377719
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:

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11158515	0.87[CHB][hapmap]
rs11158518	0.87[CHB][hapmap];0.84[MEX][hapmap]
rs11626911	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs11628650	0.87[CHB][hapmap]
rs12431956	0.87[CHB][hapmap]
rs1959034	0.81[CHD][hapmap]
rs2275018	0.81[ASN][1000 genomes]
rs2357003	0.83[CHD][hapmap];0.81[TSI][hapmap]
rs4902253	0.87[CHB][hapmap];0.88[MEX][hapmap]
rs55723325	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7146821	0.81[CHD][hapmap]
rs7152280	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8010312	0.82[CHB][hapmap]
rs8017009	0.87[CHB][hapmap]
rs998242	0.87[CHB][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
rs2150288	SYNE2	cis	parietal	SCAN
rs2150288	HIF1A	cis	parietal	SCAN
rs2150288	FLJ43390	cis	cerebellum	SCAN
rs2150288	SYT16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
2	chr14:64360600-64382200	Weak transcription	Psoas Muscle	Psoas
3	chr14:64360800-64377800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:64364400-64385200	Weak transcription	Pancreas	Pancrea
5	chr14:64364600-64387800	Weak transcription	HMEC	breast
6	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
7	chr14:64365200-64386200	Weak transcription	Gastric	stomach
8	chr14:64365400-64379800	Weak transcription	Fetal Thymus	thymus
9	chr14:64365400-64393600	Weak transcription	Right Ventricle	heart
10	chr14:64367400-64378000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr14:64369800-64386200	Weak transcription	Esophagus	oesophagus
12	chr14:64372200-64378000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr14:64374600-64399600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr14:64375200-64385000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr14:64375200-64395000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr14:64375200-64395200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr14:64375400-64380000	Strong transcription	Dnd41	blood
18	chr14:64375600-64381000	Weak transcription	NHEK	skin
19	chr14:64375800-64377800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr14:64375800-64378000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr14:64375800-64378400	Weak transcription	Colonic Mucosa	Colon
22	chr14:64375800-64380800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr14:64375800-64381000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr14:64375800-64384000	Weak transcription	Fetal Intestine Large	intestine
25	chr14:64375800-64384800	Weak transcription	Fetal Kidney	kidney
26	chr14:64375800-64386200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr14:64375800-64388600	Weak transcription	Hela-S3	cervix
28	chr14:64375800-64389000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr14:64375800-64393200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:64376000-64377800	Weak transcription	Brain Substantia Nigra	brain
31	chr14:64376000-64378000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr14:64376000-64378000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr14:64376000-64378000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr14:64376000-64378000	Enhancers	NHDF-Ad	bronchial
35	chr14:64376000-64378200	Enhancers	NHLF	lung
36	chr14:64376000-64383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr14:64376000-64385400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr14:64376000-64386200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr14:64376000-64386200	Weak transcription	Left Ventricle	heart
40	chr14:64376000-64389000	Weak transcription	Adipose Nuclei	Adipose
41	chr14:64376000-64389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr14:64376000-64389600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr14:64376000-64389600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr14:64376000-64391200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr14:64376000-64399200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr14:64376000-64399600	Weak transcription	Small Intestine	intestine
47	chr14:64376000-64399800	Weak transcription	Primary T cells from cord blood	blood
48	chr14:64376000-64416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr14:64376200-64379800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr14:64376200-64399400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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