Variant report

Variant	rs1255990
Chromosome Location	chr14:64661523-64661524
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	BACH1	chr14:64661180-64661556	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFF	chr14:64661173-64661539	K562	blood:	n/a	n/a
3	BACH1	chr14:64661252-64661817	K562	blood:	n/a	n/a
4	MAFK	chr14:64661186-64661532	K562	blood:	n/a	chr14:64661344-64661354 chr14:64661343-64661358 chr14:64661348-64661359 chr14:64661345-64661354 chr14:64661348-64661359
5	RCOR1	chr14:64661184-64661788	K562	blood:	n/a	n/a
6	MAFK	chr14:64661327-64661531	H1-hESC	embryonic stem cell:	n/a	chr14:64661344-64661354 chr14:64661343-64661358 chr14:64661348-64661359 chr14:64661345-64661354 chr14:64661348-64661359

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64660992..64662814-chr14:64664224..64665884,2	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10148269	0.84[CHB][hapmap]
rs10162323	0.88[CEU][hapmap]
rs1152578	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1152579	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1152582	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1152588	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1152589	0.94[CHB][hapmap]
rs1152590	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.83[AMR][1000 genomes]
rs1152591	0.89[CHB][hapmap]
rs1152592	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]
rs1152593	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1152594	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]
rs1152595	0.81[AFR][1000 genomes]
rs1152601	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12435376	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap]
rs1255984	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1255986	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1255988	0.92[ASN][1000 genomes]
rs1255991	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255992	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256036	0.84[CHB][hapmap]
rs1256037	0.83[CHB][hapmap]
rs1256038	0.84[CHB][hapmap]
rs1256048	0.84[CHB][hapmap]
rs1256056	0.84[CHB][hapmap]
rs1256059	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1256065	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1262242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1266927	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1272715	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2027094	0.90[CEU][hapmap]
rs2256191	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs2738413	0.89[CHB][hapmap]
rs2781379	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6573547	0.85[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs6573548	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs7148072	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs7229	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs872227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs915057	0.84[CHB][hapmap]
rs928554	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs960069	0.83[CHB][hapmap]
rs968257	0.84[CEU][hapmap]

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
rs1255990	SYNE2	cis	multi-tissue	Pritchard
rs1255990	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1255990	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1255990	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1255990	MTHFD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64600600-64667400	Weak transcription	Stomach Mucosa	stomach
2	chr14:64636800-64662600	Weak transcription	Psoas Muscle	Psoas
3	chr14:64637400-64663600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr14:64640000-64663400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr14:64645800-64663600	Weak transcription	Colonic Mucosa	Colon
6	chr14:64650800-64661600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr14:64650800-64663200	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr14:64650800-64671800	Strong transcription	Liver	Liver
9	chr14:64651600-64662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr14:64652000-64662800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr14:64652800-64666200	Strong transcription	Dnd41	blood
12	chr14:64653000-64664000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr14:64653600-64663400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr14:64655800-64663400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr14:64655800-64663600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr14:64656400-64663400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr14:64657600-64663400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr14:64657600-64663400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr14:64657800-64662600	Weak transcription	Fetal Brain Male	brain
20	chr14:64657800-64662600	Weak transcription	Fetal Brain Female	brain
21	chr14:64657800-64663600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr14:64658200-64663200	Weak transcription	Thymus	Thymus
23	chr14:64658200-64667000	Weak transcription	Esophagus	oesophagus
24	chr14:64658600-64663200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr14:64659000-64662000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr14:64659200-64662600	Weak transcription	Brain Germinal Matrix	brain
27	chr14:64659200-64663400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr14:64659200-64663400	Weak transcription	NH-A	brain
29	chr14:64659200-64663400	Weak transcription	NHLF	lung
30	chr14:64659200-64663600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr14:64659600-64661600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr14:64659600-64662000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr14:64659600-64662600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr14:64659600-64663400	Weak transcription	HMEC	breast
35	chr14:64659800-64662600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr14:64659800-64663600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr14:64660000-64662000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr14:64660000-64662800	Enhancers	Placenta	Placenta
39	chr14:64660000-64663000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr14:64660000-64663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr14:64660000-64663400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr14:64660000-64663600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr14:64660000-64663800	Weak transcription	Aorta	Aorta
44	chr14:64660200-64661600	Weak transcription	Primary T cells from cord blood	blood
45	chr14:64660200-64662200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr14:64660200-64662400	Weak transcription	Lung	lung
47	chr14:64660200-64662600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:64660200-64663400	Weak transcription	Adipose Nuclei	Adipose
49	chr14:64660200-64663400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr14:64660200-64663400	Weak transcription	Fetal Stomach	stomach

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