Variant report

Variant	rs4986938
Chromosome Location	chr14:64699816-64699817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64698101..64700318-chr14:64700621..64702248,2	MCF-7	breast:
2	chr14:64694405..64698467-chr14:64698699..64701055,4	MCF-7	breast:
3	chr14:64681860..64684849-chr14:64698718..64700886,3	MCF-7	breast:
4	chr14:64699270..64701391-chr14:64702522..64704154,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12435857	0.87[GIH][hapmap]
rs13329021	0.84[EUR][1000 genomes]
rs17179404	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs17179740	0.81[CEU][hapmap]
rs17751454	0.80[CHB][hapmap]
rs17766755	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs2772163	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs3020443	0.80[CHB][hapmap]
rs3783736	0.81[CEU][hapmap];0.89[MEX][hapmap]
rs4365213	0.86[GIH][hapmap]
rs6573549	0.82[GIH][hapmap]
rs72720395	0.86[ASN][1000 genomes]
rs8006145	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs867443	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9919904	0.80[CHB][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4986938	SYNE2	cis	multi-tissue	Pritchard
rs4986938	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs4986938	SYNE2	cis	parietal	SCAN
rs4986938	MTHFD1	cis	parietal	SCAN
rs4986938	KCNH5	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr14:64674800-64700000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr14:64674800-64700600	Strong transcription	Fetal Intestine Large	intestine
4	chr14:64688600-64700000	Strong transcription	Fetal Muscle Leg	muscle
5	chr14:64688600-64700200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr14:64688800-64710600	Weak transcription	Fetal Heart	heart
7	chr14:64689200-64705400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr14:64690200-64711200	Weak transcription	Colon Smooth Muscle	Colon
9	chr14:64691600-64700800	Weak transcription	Brain Anterior Caudate	brain
10	chr14:64691600-64701000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:64691800-64701400	Weak transcription	NHEK	skin
12	chr14:64692200-64701000	Weak transcription	Brain Angular Gyrus	brain
13	chr14:64692400-64700800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr14:64692400-64701200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr14:64692600-64700400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr14:64694600-64701000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr14:64695800-64700200	Weak transcription	Fetal Brain Male	brain
18	chr14:64695800-64705800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr14:64696000-64700800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr14:64696000-64700800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr14:64696000-64701000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr14:64696000-64701200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:64696000-64701600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr14:64696000-64701800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:64696000-64701800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr14:64696000-64702800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr14:64696000-64703400	Weak transcription	Gastric	stomach
28	chr14:64696000-64705600	Weak transcription	Fetal Lung	lung
29	chr14:64696000-64705800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr14:64696200-64700400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr14:64696200-64700600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr14:64696200-64701000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr14:64696200-64702800	Weak transcription	Fetal Kidney	kidney
34	chr14:64696200-64706000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr14:64696400-64701000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr14:64696400-64703000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr14:64696400-64708200	Weak transcription	Aorta	Aorta
38	chr14:64697000-64700400	Strong transcription	Dnd41	blood
39	chr14:64697200-64702800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr14:64697600-64700800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr14:64697800-64700000	Strong transcription	Ovary	ovary
42	chr14:64697800-64700400	Strong transcription	Brain Germinal Matrix	brain
43	chr14:64698000-64700000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
44	chr14:64698200-64700600	Strong transcription	Adipose Nuclei	Adipose
45	chr14:64698200-64700800	Enhancers	HUVEC	blood vessel
46	chr14:64698200-64701600	Weak transcription	Colonic Mucosa	Colon
47	chr14:64698400-64700000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr14:64698400-64700000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr14:64698400-64700600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr14:64698400-64705600	Weak transcription	Primary T cells fromperipheralblood	blood

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