Variant report

Variant	rs1256062
Chromosome Location	chr14:64703318-64703319
allele	A/G
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:
4	chr14:64701804..64703412-chr14:64765136..64766748,2	MCF-7	breast:

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

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10144225	0.91[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs1048315	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1109056	0.89[AFR][1000 genomes]
rs1152583	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1152587	0.83[ASN][1000 genomes]
rs11625778	0.81[JPT][hapmap]
rs1256050	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1256064	0.88[GIH][hapmap]
rs1256069	0.84[ASN][1000 genomes]
rs1952585	0.91[CEU][hapmap];0.91[GIH][hapmap]
rs2274705	0.91[CEU][hapmap]
rs8003490	0.91[GIH][hapmap]
rs8017441	0.91[CEU][hapmap];0.94[GIH][hapmap]
rs944045	0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1256062	FLJ43390	cis	cerebellum	SCAN
rs1256062	FNTB	cis	cerebellum	SCAN
rs1256062	MTHFD1	cis	cerebellum	SCAN
rs1256062	FLJ43390	cis	parietal	SCAN

Chromatin state (count:42 , 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	chr14:64696000-64703400	Weak transcription	Gastric	stomach
6	chr14:64696000-64705600	Weak transcription	Fetal Lung	lung
7	chr14:64696000-64705800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr14:64696200-64706000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr14:64696400-64708200	Weak transcription	Aorta	Aorta
10	chr14:64698400-64705600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr14:64698800-64703600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:64698800-64703600	Flanking Active TSS	GM12878-XiMat	blood
13	chr14:64698800-64716600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr14:64699600-64708000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr14:64699800-64704000	Enhancers	Primary B cells from cord blood	blood
16	chr14:64699800-64705600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:64699800-64705800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:64700000-64705800	Weak transcription	Lung	lung
19	chr14:64700000-64706400	Weak transcription	Right Ventricle	heart
20	chr14:64700200-64703400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr14:64700400-64703800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr14:64700400-64705200	Weak transcription	Dnd41	blood
23	chr14:64700600-64703400	Weak transcription	Fetal Intestine Large	intestine
24	chr14:64700600-64703800	Weak transcription	Fetal Brain Female	brain
25	chr14:64700800-64704800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr14:64701000-64703600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr14:64701000-64703600	Enhancers	Fetal Thymus	thymus
28	chr14:64702000-64703400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr14:64702000-64703400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr14:64702000-64703400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr14:64702200-64703400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr14:64702200-64707400	Enhancers	Thymus	Thymus
33	chr14:64702400-64703400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr14:64702600-64705200	Weak transcription	Ovary	ovary
35	chr14:64702600-64705200	Weak transcription	Pancreas	Pancrea
36	chr14:64702600-64706800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr14:64702600-64715400	Weak transcription	Fetal Stomach	stomach
38	chr14:64703000-64703400	Enhancers	Spleen	Spleen
39	chr14:64703000-64703600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr14:64703200-64704800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr14:64703200-64706000	Enhancers	Primary B cells from peripheral blood	blood
42	chr14:64703200-64716800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links