Variant report

Variant	rs12888000
Chromosome Location	chr14:81882643-81882644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:81684550..81687395-chr14:81881105..81883883,2	K562	blood:
2	chr14:81871880..81873578-chr14:81882062..81884053,2	MCF-7	breast:
3	chr14:81862798..81865439-chr14:81880673..81882798,2	K562	blood:
4	chr14:81870339..81872408-chr14:81882068..81884278,2	K562	blood:
5	chr14:81880605..81883337-chr14:81885961..81888667,2	K562	blood:
6	chr14:81881608..81884227-chr14:81901358..81903544,2	K562	blood:

Variant related genes	Relation type
ENSG00000165417	Chromatin interaction
ENSG00000140022	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10145634	0.85[JPT][hapmap]
rs10147025	0.85[JPT][hapmap]
rs10151523	0.80[JPT][hapmap]
rs11625151	0.85[JPT][hapmap]
rs12435104	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889412	0.86[ASN][1000 genomes]
rs12895006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896506	0.88[ASN][1000 genomes]
rs1569011	0.85[JPT][hapmap]
rs17638807	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2145122	0.85[JPT][hapmap]
rs34596952	0.81[ASN][1000 genomes]
rs3844532	0.89[GIH][hapmap];0.85[JPT][hapmap]
rs3853417	0.80[JPT][hapmap]
rs3891132	0.85[JPT][hapmap]
rs3901125	0.82[ASN][1000 genomes]
rs3908315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915221	0.89[GIH][hapmap];0.85[JPT][hapmap]
rs4089876	0.85[JPT][hapmap]
rs6574652	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7160190	0.85[JPT][hapmap]
rs7492313	0.80[JPT][hapmap]
rs8014043	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8021742	0.85[JPT][hapmap]
rs9323700	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3358936	chr14:81786719-81928269	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv902119	chr14:81810945-81884857	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1047694	chr14:81831147-82534026	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv542145	chr14:81831147-82534026	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv510645	chr14:81874624-81907004	Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
6	esv1823944	chr14:81878972-81882643	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
7	esv1807931	chr14:81878972-81908605	Bivalent Enhancer Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
8	esv1842834	chr14:81878972-81908605	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	esv1844298	chr14:81878972-81908605	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12888000	NGB	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81836400-81885800	Weak transcription	Gastric	stomach
2	chr14:81852800-81899800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:81861400-81889400	Weak transcription	Fetal Kidney	kidney
4	chr14:81864400-81893600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr14:81865000-81884600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr14:81865000-81885600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr14:81865000-81889400	Weak transcription	Ovary	ovary
8	chr14:81865000-81892400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr14:81867600-81892000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr14:81867800-81889800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr14:81868400-81884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr14:81868800-81893600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr14:81873600-81886000	Weak transcription	Fetal Muscle Leg	muscle
14	chr14:81874000-81882800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr14:81874800-81892600	Weak transcription	Hela-S3	cervix
16	chr14:81876800-81884200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr14:81879400-81884600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:81879400-81885800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr14:81880600-81883000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:81880800-81884800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr14:81881000-81882800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr14:81881000-81884400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr14:81881000-81886200	Weak transcription	NHEK	skin
24	chr14:81881000-81892000	Weak transcription	HMEC	breast
25	chr14:81881400-81882800	Enhancers	Fetal Intestine Large	intestine
26	chr14:81881400-81882800	Weak transcription	Placenta	Placenta
27	chr14:81881400-81883000	Enhancers	Fetal Intestine Small	intestine
28	chr14:81881400-81884200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr14:81881400-81886000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr14:81881600-81882800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr14:81881600-81883800	Enhancers	Primary hematopoietic stem cells	blood
32	chr14:81881600-81886200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr14:81881600-81888400	Weak transcription	Psoas Muscle	Psoas
34	chr14:81882200-81882800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr14:81882200-81882800	Enhancers	HepG2	liver
36	chr14:81882200-81883600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr14:81882200-81883600	Enhancers	Spleen	Spleen
38	chr14:81882400-81883000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr14:81882400-81883200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr14:81882600-81883000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr14:81882600-81883200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr14:81882600-81883600	Enhancers	Brain Anterior Caudate	brain
43	chr14:81882600-81884000	Enhancers	Adipose Nuclei	Adipose
44	chr14:81882600-81884400	Genic enhancers	K562	blood
45	chr14:81882600-81886200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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