Variant report

Variant	rs1152595
Chromosome Location	chr14:64674981-64674982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr14:64674974-64675284	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr14:64674979-64675316	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr14:64674901-64675429	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64667402..64671365-chr14:64674791..64677546,5	MCF-7	breast:
2	chr14:64662914..64664547-chr14:64673887..64676659,2	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1152582	0.80[ASN][1000 genomes]
rs1152586	0.81[ASN][1000 genomes]
rs1152589	0.82[ASN][1000 genomes]
rs1152590	0.85[ASN][1000 genomes]
rs1152591	0.84[ASN][1000 genomes]
rs1152592	0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1152593	0.88[ASN][1000 genomes]
rs1152594	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1152601	0.88[AFR][1000 genomes]
rs1255990	0.81[AFR][1000 genomes]
rs1255991	0.84[AFR][1000 genomes]
rs1255992	0.84[AFR][1000 genomes]
rs2738413	0.81[ASN][1000 genomes]
rs928554	0.81[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	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
2	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv902021	chr14:64647646-64715794	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1152595	SYNE2	cis	multi-tissue	Pritchard
rs1152595	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs1152595	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1152595	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1152595	ESR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64660800-64682600	Weak transcription	Hela-S3	cervix
2	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr14:64661600-64675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:64661800-64675400	Weak transcription	NHEK	skin
5	chr14:64661800-64675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr14:64662400-64675200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
8	chr14:64664200-64675000	Weak transcription	Aorta	Aorta
9	chr14:64664200-64675000	Weak transcription	Colonic Mucosa	Colon
10	chr14:64664200-64675400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr14:64664200-64676200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr14:64664200-64698600	Weak transcription	HMEC	breast
13	chr14:64664400-64675800	Weak transcription	NHLF	lung
14	chr14:64665000-64675600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr14:64665200-64676600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr14:64665400-64675400	Weak transcription	Brain Anterior Caudate	brain
17	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr14:64666000-64675200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr14:64666200-64675400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr14:64666200-64675800	Weak transcription	Brain Angular Gyrus	brain
21	chr14:64666200-64678600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr14:64666200-64686000	Weak transcription	Brain Hippocampus Middle	brain
23	chr14:64666800-64699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr14:64667200-64675000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr14:64667200-64675000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr14:64667400-64675000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr14:64667400-64679200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr14:64667400-64690200	Weak transcription	HepG2	liver
29	chr14:64667600-64675200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr14:64667600-64676000	Weak transcription	Psoas Muscle	Psoas
31	chr14:64667600-64676000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr14:64667600-64686200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr14:64667800-64675000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr14:64667800-64675400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr14:64667800-64675400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr14:64667800-64676400	Weak transcription	Brain Substantia Nigra	brain
37	chr14:64667800-64678600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr14:64668000-64675000	Weak transcription	Brain Germinal Matrix	brain
39	chr14:64668000-64675000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr14:64668200-64675400	Weak transcription	Stomach Mucosa	stomach
41	chr14:64668200-64675600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr14:64668400-64675000	Weak transcription	Fetal Heart	heart
43	chr14:64668800-64676000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr14:64669000-64675000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr14:64669000-64675000	Weak transcription	Lung	lung
46	chr14:64669200-64682000	Weak transcription	Fetal Brain Male	brain
47	chr14:64669800-64675200	Weak transcription	Fetal Lung	lung
48	chr14:64669800-64675800	Weak transcription	Ovary	ovary
49	chr14:64670600-64675000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr14:64672800-64696600	Strong transcription	Primary T cells fromperipheralblood	blood

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