Variant report

Variant	rs7153101
Chromosome Location	chr14:64380896-64380897
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10873172	0.82[CEU][hapmap]
rs11158512	0.84[AMR][1000 genomes]
rs11158516	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12435958	0.85[MEX][hapmap]
rs12587472	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12588087	0.82[AMR][1000 genomes]
rs12894053	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12894864	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1953241	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs1959034	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1959035	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2210650	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2275018	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2357001	0.90[MEX][hapmap]
rs2357002	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2357003	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34780876	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4902247	0.84[AMR][1000 genomes]
rs4902248	0.84[AMR][1000 genomes]
rs6573534	0.82[AMR][1000 genomes]
rs7145302	0.90[MEX][hapmap]
rs7146821	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7157314	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7157323	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7160127	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7493416	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8005899	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8015158	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8015354	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8022917	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs945030	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs954730	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9707224	0.84[AMR][1000 genomes]
rs998241	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7153101	SYNE2	cis	parietal	SCAN
rs7153101	HIF1A	cis	parietal	SCAN
rs7153101	SYT16	cis	parietal	SCAN
rs7153101	SYNE2	cis	cerebellum	SCAN
rs7153101	FLJ43390	cis	cerebellum	SCAN

Chromatin state (count:74 , 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	chr14:64364400-64385200	Weak transcription	Pancreas	Pancrea
4	chr14:64364600-64387800	Weak transcription	HMEC	breast
5	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
6	chr14:64365200-64386200	Weak transcription	Gastric	stomach
7	chr14:64365400-64393600	Weak transcription	Right Ventricle	heart
8	chr14:64369800-64386200	Weak transcription	Esophagus	oesophagus
9	chr14:64374600-64399600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr14:64375200-64385000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr14:64375200-64395000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr14:64375200-64395200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr14:64375600-64381000	Weak transcription	NHEK	skin
14	chr14:64375800-64381000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr14:64375800-64384000	Weak transcription	Fetal Intestine Large	intestine
16	chr14:64375800-64384800	Weak transcription	Fetal Kidney	kidney
17	chr14:64375800-64386200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr14:64375800-64388600	Weak transcription	Hela-S3	cervix
19	chr14:64375800-64389000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr14:64375800-64393200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr14:64376000-64383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr14:64376000-64385400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr14:64376000-64386200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr14:64376000-64386200	Weak transcription	Left Ventricle	heart
25	chr14:64376000-64389000	Weak transcription	Adipose Nuclei	Adipose
26	chr14:64376000-64389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr14:64376000-64389600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr14:64376000-64389600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr14:64376000-64391200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:64376000-64399200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr14:64376000-64399600	Weak transcription	Small Intestine	intestine
32	chr14:64376000-64399800	Weak transcription	Primary T cells from cord blood	blood
33	chr14:64376000-64416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr14:64376200-64399400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr14:64376400-64394000	Weak transcription	Lung	lung
36	chr14:64377600-64386200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:64377600-64388000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr14:64377600-64389400	Weak transcription	Fetal Intestine Small	intestine
39	chr14:64378000-64383600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr14:64378000-64384600	Weak transcription	Stomach Mucosa	stomach
41	chr14:64378000-64385200	Weak transcription	Ovary	ovary
42	chr14:64378000-64386000	Weak transcription	Fetal Stomach	stomach
43	chr14:64378000-64386200	Weak transcription	Fetal Muscle Leg	muscle
44	chr14:64378000-64389400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr14:64378000-64394800	Weak transcription	Fetal Heart	heart
46	chr14:64378000-64404800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr14:64378000-64416200	Weak transcription	Fetal Lung	lung
48	chr14:64378200-64381000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr14:64378200-64385800	Weak transcription	Aorta	Aorta
50	chr14:64378200-64389200	Weak transcription	Brain Germinal Matrix	brain

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