Variant report

Variant	rs1514299
Chromosome Location	chr4:128545466-128545467
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:128543078..128545882-chr4:128552977..128554729,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164066	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10023894	0.82[ASN][1000 genomes]
rs1018289	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs10493147	0.83[CHB][hapmap]
rs10857125	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11098931	0.89[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs11098933	0.92[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1159021	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs1159022	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11732886	0.80[CEU][hapmap]
rs11946559	0.84[ASN][1000 genomes]
rs12331481	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12509562	0.86[EUR][1000 genomes]
rs12639763	0.84[ASN][1000 genomes]
rs13126673	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13151291	0.85[CEU][hapmap]
rs1380156	0.83[CHB][hapmap]
rs1399210	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1399211	0.88[EUR][1000 genomes]
rs1459048	0.83[CHB][hapmap]
rs1459049	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1459050	0.83[CHB][hapmap]
rs1514298	0.89[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1903104	0.83[CHB][hapmap]
rs1913464	0.87[EUR][1000 genomes]
rs2048685	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048686	0.85[EUR][1000 genomes]
rs2085655	0.83[CHB][hapmap]
rs2125573	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2255457	0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs2305957	0.83[CHB][hapmap]
rs2391188	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2391189	0.87[EUR][1000 genomes]
rs28656192	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3214038	0.83[CHB][hapmap]
rs34066758	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3749507	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4340805	0.83[ASN][1000 genomes]
rs4543128	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4833380	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4833383	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4833384	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833386	0.88[ASN][1000 genomes]
rs4833391	0.83[CHB][hapmap]
rs4834206	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834210	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4834211	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs4834214	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap]
rs4834217	0.83[CHB][hapmap]
rs6534630	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6534631	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs6534632	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534633	0.85[CEU][hapmap]
rs6828511	0.81[CEU][hapmap]
rs6847056	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847397	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs6854119	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6858855	0.81[CEU][hapmap]
rs7664217	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678085	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs7679782	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7683627	0.81[CEU][hapmap]
rs7686395	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs7692114	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs769293	0.83[CHB][hapmap]
rs7694079	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs922060	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1029214	chr4:128292215-128683123	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537247	chr4:128292215-128683123	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv879916	chr4:128422400-128694288	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1800085	chr4:128502675-128557864	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv830056	chr4:128517139-128676557	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats 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	diseases
9	nsv879918	chr4:128543742-128694288	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv879919	chr4:128543742-128697519	Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1514299	PLK4	cis	cerebellum	SCAN
rs1514299	LARP1B	cis	parietal	SCAN
rs1514299	HSPA4L	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128543600-128545600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:128543600-128545600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr4:128543600-128545600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:128543600-128545600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:128543600-128546000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:128543600-128546400	Active TSS	Brain Anterior Caudate	brain
7	chr4:128543800-128545600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:128543800-128545600	Active TSS	Brain Substantia Nigra	brain
9	chr4:128543800-128546600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:128543800-128547000	Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr4:128544000-128545600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:128544000-128545800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:128544000-128545800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr4:128544000-128546000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:128544000-128546000	Active TSS	Brain Angular Gyrus	brain
16	chr4:128544000-128546400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:128544200-128545600	Active TSS	Fetal Brain Male	brain
18	chr4:128544200-128546200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:128544200-128546200	Active TSS	HMEC	breast
20	chr4:128544200-128546200	Active TSS	NH-A	brain
21	chr4:128544600-128545600	Active TSS	Brain Cingulate Gyrus	brain
22	chr4:128545000-128545600	Active TSS	Brain Hippocampus Middle	brain
23	chr4:128545000-128546400	Active TSS	Brain Germinal Matrix	brain
24	chr4:128545000-128547600	Active TSS	Fetal Brain Female	brain
25	chr4:128545000-128550600	Weak transcription	Esophagus	oesophagus
26	chr4:128545200-128545600	Flanking Active TSS	Fetal Lung	lung
27	chr4:128545200-128546200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:128545200-128552400	Weak transcription	Psoas Muscle	Psoas
29	chr4:128545400-128545600	Flanking Bivalent TSS/Enh	ES-WA7 Cell Line	embryonic stem cell
30	chr4:128545400-128545600	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
31	chr4:128545400-128545600	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr4:128545400-128545600	Flanking Active TSS	Fetal Stomach	stomach
33	chr4:128545400-128545600	Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links