Variant report

Variant	rs1255991
Chromosome Location	chr14:64661642-64661643
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	chr14:64661252-64661817	K562	blood:	n/a	n/a
2	RCOR1	chr14:64661184-64661788	K562	blood:	n/a	n/a
3	POLR2A	chr14:64661633-64662948	GM12878	blood:	n/a	n/a

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: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1152590	0.82[AMR][1000 genomes]
rs1152592	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1152593	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1152594	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1152595	0.84[AFR][1000 genomes]
rs1152601	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1255984	0.88[ASN][1000 genomes]
rs1255986	0.92[ASN][1000 genomes]
rs1255988	0.92[ASN][1000 genomes]
rs1255990	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255992	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1262242	0.91[AFR][1000 genomes];0.93[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	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2256191	0.80[EUR][1000 genomes]
rs2781379	0.83[EUR][1000 genomes]
rs872227	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1255991	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs1255991	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1255991	SYNE2	cis	multi-tissue	Pritchard
rs1255991	SYNE2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 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	chr14:64650800-64663200	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr14:64650800-64671800	Strong transcription	Liver	Liver
8	chr14:64651600-64662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr14:64652000-64662800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:64652800-64666200	Strong transcription	Dnd41	blood
11	chr14:64653000-64664000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr14:64653600-64663400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr14:64655800-64663400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr14:64655800-64663600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr14:64656400-64663400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr14:64657600-64663400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr14:64657600-64663400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr14:64657800-64662600	Weak transcription	Fetal Brain Male	brain
19	chr14:64657800-64662600	Weak transcription	Fetal Brain Female	brain
20	chr14:64657800-64663600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr14:64658200-64663200	Weak transcription	Thymus	Thymus
22	chr14:64658200-64667000	Weak transcription	Esophagus	oesophagus
23	chr14:64658600-64663200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr14:64659000-64662000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr14:64659200-64662600	Weak transcription	Brain Germinal Matrix	brain
26	chr14:64659200-64663400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:64659200-64663400	Weak transcription	NH-A	brain
28	chr14:64659200-64663400	Weak transcription	NHLF	lung
29	chr14:64659200-64663600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr14:64659600-64662000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:64659600-64662600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr14:64659600-64663400	Weak transcription	HMEC	breast
33	chr14:64659800-64662600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr14:64659800-64663600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr14:64660000-64662000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr14:64660000-64662800	Enhancers	Placenta	Placenta
37	chr14:64660000-64663000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr14:64660000-64663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:64660000-64663400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr14:64660000-64663600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr14:64660000-64663800	Weak transcription	Aorta	Aorta
42	chr14:64660200-64662200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr14:64660200-64662400	Weak transcription	Lung	lung
44	chr14:64660200-64662600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr14:64660200-64663400	Weak transcription	Adipose Nuclei	Adipose
46	chr14:64660200-64663400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr14:64660200-64663400	Weak transcription	Fetal Stomach	stomach
48	chr14:64660400-64662800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:64660400-64663400	Enhancers	Fetal Heart	heart
50	chr14:64660400-64663400	Weak transcription	Fetal Muscle Leg	muscle

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