Variant report

Variant	rs1399210
Chromosome Location	chr4:128545830-128545831
allele	A/T
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: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10023894	0.82[ASN][1000 genomes]
rs1018289	0.85[EUR][1000 genomes]
rs10857125	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11098931	0.85[EUR][1000 genomes]
rs11098933	0.84[EUR][1000 genomes]
rs1159021	0.85[ASN][1000 genomes]
rs1159022	0.84[ASN][1000 genomes]
rs11946559	0.84[ASN][1000 genomes]
rs12331481	0.83[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	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1399211	0.88[EUR][1000 genomes]
rs1459049	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1514298	0.86[EUR][1000 genomes]
rs1514299	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913464	0.87[EUR][1000 genomes]
rs2048685	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048686	0.85[EUR][1000 genomes]
rs2125573	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2255457	0.87[EUR][1000 genomes]
rs2391188	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2391189	0.87[EUR][1000 genomes]
rs28656192	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34066758	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3749507	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4340805	0.83[ASN][1000 genomes]
rs4543128	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4833380	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4833383	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]
rs4834206	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834210	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4834211	0.85[ASN][1000 genomes]
rs6534630	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6534631	0.87[EUR][1000 genomes]
rs6534632	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6847056	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847397	0.86[EUR][1000 genomes]
rs6854119	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7664217	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679782	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7686395	0.87[EUR][1000 genomes]
rs7692114	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7694079	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128543600-128546000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:128543600-128546400	Active TSS	Brain Anterior Caudate	brain
3	chr4:128543800-128546600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:128543800-128547000	Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr4:128544000-128546000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:128544000-128546000	Active TSS	Brain Angular Gyrus	brain
7	chr4:128544000-128546400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:128544200-128546200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:128544200-128546200	Active TSS	HMEC	breast
10	chr4:128544200-128546200	Active TSS	NH-A	brain
11	chr4:128545000-128546400	Active TSS	Brain Germinal Matrix	brain
12	chr4:128545000-128547600	Active TSS	Fetal Brain Female	brain
13	chr4:128545000-128550600	Weak transcription	Esophagus	oesophagus
14	chr4:128545200-128546200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:128545200-128552400	Weak transcription	Psoas Muscle	Psoas
16	chr4:128545600-128546200	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr4:128545600-128553400	Weak transcription	Fetal Brain Male	brain
18	chr4:128545800-128546200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:128545800-128546200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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