Variant report

Variant	rs1256063
Chromosome Location	chr14:64702217-64702218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:64698101..64700318-chr14:64700621..64702248,2	MCF-7	breast:
2	chr14:64701273..64703199-chr14:64731826..64734576,2	MCF-7	breast:
3	chr14:64701411..64702290-chr14:64764943..64765931,3	MCF-7	breast:
4	chr14:64690892..64693639-chr14:64700268..64702860,3	MCF-7	breast:
5	chr14:64701764..64704749-chr14:64970192..64972112,2	MCF-7	breast:
6	chr14:64682391..64683248-chr14:64701375..64702283,4	MCF-7	breast:
7	chr14:64701659..64704399-chr14:64760187..64762657,2	MCF-7	breast:
8	chr14:64701804..64703412-chr14:64765136..64766748,2	MCF-7	breast:

No data

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

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1255997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1256028	0.86[EUR][1000 genomes]
rs1256052	1.00[AFR][1000 genomes]
rs1271570	1.00[AFR][1000 genomes]
rs17751556	1.00[ASW][hapmap]
rs2738412	1.00[AFR][1000 genomes]
rs3853411	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1050378	chr14:64686543-64703012	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1256063	MTHFD1	cis	parietal	SCAN
rs1256063	MTHFD1	cis	cerebellum	SCAN
rs1256063	SYNE2	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

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	chr14:64696000-64702800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr14:64696000-64703400	Weak transcription	Gastric	stomach
7	chr14:64696000-64705600	Weak transcription	Fetal Lung	lung
8	chr14:64696000-64705800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr14:64696200-64702800	Weak transcription	Fetal Kidney	kidney
10	chr14:64696200-64706000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr14:64696400-64703000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr14:64696400-64708200	Weak transcription	Aorta	Aorta
13	chr14:64697200-64702800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr14:64698400-64705600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr14:64698600-64702600	Strong transcription	Fetal Stomach	stomach
16	chr14:64698800-64702400	Enhancers	Primary B cells from peripheral blood	blood
17	chr14:64698800-64702600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr14:64698800-64703600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr14:64698800-64703600	Flanking Active TSS	GM12878-XiMat	blood
20	chr14:64698800-64716600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr14:64699600-64708000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr14:64699800-64704000	Enhancers	Primary B cells from cord blood	blood
23	chr14:64699800-64705600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:64699800-64705800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:64700000-64705800	Weak transcription	Lung	lung
26	chr14:64700000-64706400	Weak transcription	Right Ventricle	heart
27	chr14:64700200-64703400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr14:64700400-64702600	Enhancers	Pancreas	Pancrea
29	chr14:64700400-64703800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr14:64700400-64705200	Weak transcription	Dnd41	blood
31	chr14:64700600-64702400	Bivalent Enhancer	NH-A	brain
32	chr14:64700600-64703000	Weak transcription	Adipose Nuclei	Adipose
33	chr14:64700600-64703400	Weak transcription	Fetal Intestine Large	intestine
34	chr14:64700600-64703800	Weak transcription	Fetal Brain Female	brain
35	chr14:64700800-64702600	Enhancers	Duodenum Mucosa	Duodenum
36	chr14:64700800-64704800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr14:64701000-64702400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:64701000-64702600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
39	chr14:64701000-64703600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr14:64701000-64703600	Enhancers	Fetal Thymus	thymus
41	chr14:64701200-64702600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr14:64701200-64702800	Enhancers	Spleen	Spleen
43	chr14:64701400-64702400	Enhancers	HMEC	breast
44	chr14:64701400-64702600	Enhancers	Ovary	ovary
45	chr14:64701600-64702600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr14:64701600-64702600	Enhancers	Fetal Muscle Trunk	muscle
47	chr14:64701800-64703200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr14:64701800-64703200	Strong transcription	Brain Germinal Matrix	brain
49	chr14:64702000-64703400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr14:64702000-64703400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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