Variant report

Variant	rs1152592
Chromosome Location	chr14:64676098-64676099
allele	C/T
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	SPI1	chr14:64675836-64676810	GM12878	blood:	n/a	chr14:64676369-64676376
2	SPI1	chr14:64676045-64676555	GM12878	blood:	n/a	chr14:64676369-64676376
3	MAZ	chr14:64675819-64676888	IMR90	lung:	n/a	n/a
4	RUNX3	chr14:64676093-64676603	GM12878	blood:	n/a	n/a
5	PAX5	chr14:64676067-64676509	GM12878	blood:	n/a	chr14:64676367-64676376

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: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10148269	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs10162323	0.84[CEU][hapmap]
rs1152577	0.81[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	0.85[ASN][1000 genomes]
rs1152588	0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1152589	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1152590	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1152591	0.89[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs1152593	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1152594	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]
rs1152595	0.95[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1152601	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12435376	0.84[CEU][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs1255984	0.94[CHB][hapmap]
rs1255986	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1255990	0.88[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];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255991	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255992	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][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]
rs1256065	0.84[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1262242	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1266927	0.81[ASN][1000 genomes]
rs1269056	0.85[JPT][hapmap]
rs1272715	0.81[EUR][1000 genomes]
rs1760988	0.82[ASN][1000 genomes]
rs2027094	0.90[CEU][hapmap]
rs2256191	0.88[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs2738413	0.89[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2781379	0.88[CEU][hapmap]
rs2987983	0.80[MEX][hapmap]
rs6573547	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs6573548	0.84[CEU][hapmap];0.90[MEX][hapmap]
rs7148072	0.84[CEU][hapmap];0.90[MEX][hapmap]
rs7229	0.84[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs872227	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs915057	0.84[CHB][hapmap]
rs928554	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs944046	0.83[ASN][1000 genomes]
rs944047	0.83[ASN][1000 genomes]
rs960069	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs968257	0.96[CEU][hapmap];0.84[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
rs1152592	SYNE2	cis	multi-tissue	Pritchard
rs1152592	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1152592	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1152592	MTHFD1	cis	cerebellum	SCAN

Chromatin state (count:113 , 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	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
3	chr14:64664200-64676200	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr14:64664200-64698600	Weak transcription	HMEC	breast
5	chr14:64665200-64676600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr14:64666200-64678600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:64666200-64686000	Weak transcription	Brain Hippocampus Middle	brain
9	chr14:64666800-64699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr14:64667400-64679200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:64667400-64690200	Weak transcription	HepG2	liver
12	chr14:64667600-64686200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr14:64667800-64676400	Weak transcription	Brain Substantia Nigra	brain
14	chr14:64667800-64678600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr14:64669200-64682000	Weak transcription	Fetal Brain Male	brain
16	chr14:64672800-64696600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr14:64673800-64676400	Weak transcription	Primary B cells from cord blood	blood
18	chr14:64674000-64680400	Strong transcription	Fetal Intestine Small	intestine
19	chr14:64674600-64696000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr14:64674600-64696200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr14:64674600-64696400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:64674600-64699800	Strong transcription	Liver	Liver
23	chr14:64674800-64676400	Enhancers	Right Atrium	heart
24	chr14:64674800-64676400	Genic enhancers	Thymus	Thymus
25	chr14:64674800-64676600	Strong transcription	Esophagus	oesophagus
26	chr14:64674800-64677000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:64674800-64677000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr14:64674800-64677200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr14:64674800-64677200	Genic enhancers	Left Ventricle	heart
30	chr14:64674800-64678400	Genic enhancers	Fetal Muscle Leg	muscle
31	chr14:64674800-64679200	Strong transcription	Gastric	stomach
32	chr14:64674800-64680800	Strong transcription	Placenta	Placenta
33	chr14:64674800-64683400	Strong transcription	Fetal Brain Female	brain
34	chr14:64674800-64683800	Strong transcription	Adipose Nuclei	Adipose
35	chr14:64674800-64684400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr14:64674800-64686800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr14:64674800-64689000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr14:64674800-64689000	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr14:64674800-64692400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr14:64674800-64692600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr14:64674800-64692800	Strong transcription	Primary T cells from cord blood	blood
42	chr14:64674800-64695800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr14:64674800-64696000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr14:64674800-64696000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr14:64674800-64696000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr14:64674800-64696200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr14:64674800-64696200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr14:64674800-64696200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr14:64674800-64696400	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr14:64674800-64696400	Strong transcription	Dnd41	blood

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