Variant report

Variant	rs12588807
Chromosome Location	chr14:64363070-64363071
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64319794..64321904-chr14:64361235..64363695,2	MCF-7	breast:
2	chr14:64319630..64322805-chr14:64362843..64364773,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11158519	0.86[MEX][hapmap]
rs11158520	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11850711	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12588955	0.86[ASN][1000 genomes]
rs12589453	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12878037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878348	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879374	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12881942	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12882429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12888489	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12888712	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12891546	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12894963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751301	1.00[CEU][hapmap]
rs17824268	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs33976862	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34328391	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34451919	0.86[ASN][1000 genomes]
rs34556545	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34561759	1.00[ASN][1000 genomes]
rs35009554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033077	0.83[ASN][1000 genomes]
rs35168922	1.00[ASN][1000 genomes]
rs35302448	1.00[ASN][1000 genomes]
rs35581544	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35984502	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818774	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4459477	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs4899120	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4902250	1.00[ASN][1000 genomes]
rs6573539	0.94[EUR][1000 genomes]
rs66684280	1.00[ASN][1000 genomes]
rs67289344	1.00[ASN][1000 genomes]
rs71416319	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144308	0.86[ASN][1000 genomes]
rs7401191	1.00[ASN][1000 genomes]
rs8015210	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs8023195	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv564904	chr14:64346190-64416898	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1793389	chr14:64346190-64457224	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv826965	chr14:64360774-64366612	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12588807	C14orf50	cis	lymphoblastoid	seeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64337000-64365200	Weak transcription	Fetal Thymus	thymus
2	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
3	chr14:64339400-64366800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr14:64341400-64366800	Weak transcription	Primary T cells from cord blood	blood
5	chr14:64342800-64368400	Weak transcription	Esophagus	oesophagus
6	chr14:64349400-64366600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr14:64349600-64366000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:64352800-64366800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr14:64357000-64363600	Enhancers	Liver	Liver
10	chr14:64357800-64364800	Weak transcription	Fetal Intestine Large	intestine
11	chr14:64357800-64366600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr14:64358000-64364400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr14:64358200-64375800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr14:64358200-64377600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:64358400-64365400	Enhancers	Adipose Nuclei	Adipose
16	chr14:64358400-64366000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:64358600-64364400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:64358600-64365800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr14:64358800-64377600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:64359000-64366400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr14:64359000-64367800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr14:64359800-64364200	Weak transcription	Dnd41	blood
23	chr14:64360000-64365000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr14:64360600-64364200	Weak transcription	Fetal Brain Male	brain
25	chr14:64360600-64364200	Weak transcription	Spleen	Spleen
26	chr14:64360600-64365600	Enhancers	Fetal Lung	lung
27	chr14:64360600-64382200	Weak transcription	Psoas Muscle	Psoas
28	chr14:64360800-64364200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr14:64360800-64364200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr14:64360800-64364400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr14:64360800-64367000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr14:64360800-64374200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr14:64360800-64377800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr14:64361000-64363200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr14:64361000-64364200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr14:64361200-64373600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:64361400-64363600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr14:64361400-64363600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr14:64361400-64363600	Weak transcription	Left Ventricle	heart
40	chr14:64361400-64364200	Weak transcription	Gastric	stomach
41	chr14:64361400-64369800	Weak transcription	Colonic Mucosa	Colon
42	chr14:64361800-64363200	Weak transcription	Right Atrium	heart
43	chr14:64361800-64364200	Weak transcription	Right Ventricle	heart
44	chr14:64362000-64363400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr14:64362200-64363400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr14:64362400-64363200	Weak transcription	Fetal Stomach	stomach
47	chr14:64362400-64363400	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr14:64362400-64363400	Enhancers	NHEK	skin
49	chr14:64362600-64363200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr14:64362600-64363200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links