Variant report

Variant	rs1152594
Chromosome Location	chr14:64675044-64675045
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	CTCF	chr14:64675040-64675190	HepG2	liver:	n/a	n/a
2	RAD21	chr14:64674974-64675284	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr14:64674979-64675316	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr14:64674901-64675429	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr14:64675007-64675375	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: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10148269	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs10162323	0.88[CEU][hapmap]
rs1152577	0.82[ASN][1000 genomes]
rs1152578	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1152579	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1152582	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1152586	0.84[ASN][1000 genomes]
rs1152588	0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1152589	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1152590	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1152591	0.89[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs1152592	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1152593	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152595	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1152601	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12435376	0.88[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs1255984	0.94[CHB][hapmap]
rs1255986	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1255990	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1255991	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1255992	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1256030	0.85[JPT][hapmap]
rs1256036	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs1256037	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1256038	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1256043	0.83[JPT][hapmap]
rs1256044	0.85[JPT][hapmap]
rs1256045	0.85[JPT][hapmap]
rs1256048	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs1256056	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs1256059	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1256065	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1262242	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs1266927	0.81[ASN][1000 genomes]
rs1269056	0.85[JPT][hapmap]
rs1760988	0.83[ASN][1000 genomes]
rs2027094	0.90[CEU][hapmap]
rs2256191	0.84[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs2738413	0.89[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2781379	0.84[CEU][hapmap]
rs2987983	0.80[MEX][hapmap]
rs6573547	0.84[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs6573548	0.88[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs7148072	0.88[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs7229	0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs872227	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs915057	0.84[CHB][hapmap]
rs928554	0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs944046	0.84[ASN][1000 genomes]
rs944047	0.84[ASN][1000 genomes]
rs960069	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs968257	0.92[CEU][hapmap];0.80[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1152594	SYNE2	cis	multi-tissue	Pritchard
rs1152594	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1152594	MTHFD1	cis	cerebellum	SCAN
rs1152594	MTHFD1	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	chr14:64661800-64675400	Weak transcription	NHEK	skin
3	chr14:64661800-64675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr14:64662400-64675200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
6	chr14:64664200-64675400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr14:64664200-64676200	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr14:64664200-64698600	Weak transcription	HMEC	breast
9	chr14:64664400-64675800	Weak transcription	NHLF	lung
10	chr14:64665000-64675600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:64665200-64676600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr14:64665400-64675400	Weak transcription	Brain Anterior Caudate	brain
13	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr14:64666000-64675200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr14:64666200-64675400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:64666200-64675800	Weak transcription	Brain Angular Gyrus	brain
17	chr14:64666200-64678600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr14:64666200-64686000	Weak transcription	Brain Hippocampus Middle	brain
19	chr14:64666800-64699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr14:64667400-64679200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr14:64667400-64690200	Weak transcription	HepG2	liver
22	chr14:64667600-64675200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr14:64667600-64676000	Weak transcription	Psoas Muscle	Psoas
24	chr14:64667600-64676000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr14:64667600-64686200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr14:64667800-64675400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr14:64667800-64675400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr14:64667800-64676400	Weak transcription	Brain Substantia Nigra	brain
29	chr14:64667800-64678600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr14:64668200-64675400	Weak transcription	Stomach Mucosa	stomach
31	chr14:64668200-64675600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr14:64668800-64676000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr14:64669200-64682000	Weak transcription	Fetal Brain Male	brain
34	chr14:64669800-64675200	Weak transcription	Fetal Lung	lung
35	chr14:64669800-64675800	Weak transcription	Ovary	ovary
36	chr14:64672800-64696600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr14:64673000-64675200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr14:64673000-64675600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr14:64673400-64675200	Weak transcription	Fetal Thymus	thymus
40	chr14:64673800-64676000	Weak transcription	Fetal Kidney	kidney
41	chr14:64673800-64676400	Weak transcription	Primary B cells from cord blood	blood
42	chr14:64674000-64680400	Strong transcription	Fetal Intestine Small	intestine
43	chr14:64674600-64675800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr14:64674600-64696000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr14:64674600-64696200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr14:64674600-64696400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr14:64674600-64699800	Strong transcription	Liver	Liver
48	chr14:64674800-64675400	Strong transcription	Right Ventricle	heart
49	chr14:64674800-64675400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr14:64674800-64675400	Strong transcription	Spleen	Spleen

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