Variant report

Variant	rs1256061
Chromosome Location	chr14:64703593-64703594
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64699270..64701391-chr14:64702522..64704154,2	MCF-7	breast:
2	chr14:64701764..64704749-chr14:64970192..64972112,2	MCF-7	breast:
3	chr14:64701659..64704399-chr14:64760187..64762657,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089775	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000140009	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12435857	0.88[CEU][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap]
rs1256031	0.85[JPT][hapmap]
rs1256033	0.85[JPT][hapmap]
rs1256040	0.84[JPT][hapmap]
rs17766755	0.83[GIH][hapmap]
rs4365213	0.88[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs6573549	0.81[CEU][hapmap];0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv524908	chr14:64700045-64703593	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1256061	MTHFD1	cis	parietal	SCAN
rs1256061	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs1256061	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs1256061	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs1256061	SYNE2	cis	parietal	SCAN
rs1256061	SYNE2	cis	multi-tissue	Pritchard
rs1256061	C15orf59	trans	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64688800-64710600	Weak transcription	Fetal Heart	heart
2	chr14:64689200-64705400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr14:64690200-64711200	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:64695800-64705800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr14:64696000-64705600	Weak transcription	Fetal Lung	lung
6	chr14:64696000-64705800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr14:64696200-64706000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr14:64696400-64708200	Weak transcription	Aorta	Aorta
9	chr14:64698400-64705600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr14:64698800-64703600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr14:64698800-64703600	Flanking Active TSS	GM12878-XiMat	blood
12	chr14:64698800-64716600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr14:64699600-64708000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr14:64699800-64704000	Enhancers	Primary B cells from cord blood	blood
15	chr14:64699800-64705600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr14:64699800-64705800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:64700000-64705800	Weak transcription	Lung	lung
18	chr14:64700000-64706400	Weak transcription	Right Ventricle	heart
19	chr14:64700400-64703800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr14:64700400-64705200	Weak transcription	Dnd41	blood
21	chr14:64700600-64703800	Weak transcription	Fetal Brain Female	brain
22	chr14:64700800-64704800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr14:64701000-64703600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr14:64701000-64703600	Enhancers	Fetal Thymus	thymus
25	chr14:64702200-64707400	Enhancers	Thymus	Thymus
26	chr14:64702600-64705200	Weak transcription	Ovary	ovary
27	chr14:64702600-64705200	Weak transcription	Pancreas	Pancrea
28	chr14:64702600-64706800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr14:64702600-64715400	Weak transcription	Fetal Stomach	stomach
30	chr14:64703000-64703600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr14:64703200-64704800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr14:64703200-64706000	Enhancers	Primary B cells from peripheral blood	blood
33	chr14:64703200-64716800	Weak transcription	Brain Germinal Matrix	brain
34	chr14:64703400-64703600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr14:64703400-64703600	Active TSS	Gastric	stomach
36	chr14:64703400-64703600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr14:64703400-64703800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr14:64703400-64704800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr14:64703400-64705800	Weak transcription	Spleen	Spleen

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