Variant report

Variant	rs62299414
Chromosome Location	chr4:55189540-55189541
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:55188651..55189879-chr4:55299577..55300637,10	MCF-7	breast:
2	chr4:55188876..55189604-chr4:55241739..55242312,2	MCF-7	breast:
3	chr4:55188755..55189636-chr4:55299369..55300499,5	MCF-7	breast:
4	chr4:55188742..55189647-chr4:55306683..55307683,5	K562	blood:
5	chr4:55189198..55189880-chr4:55837437..55838307,2	MCF-7	breast:
6	chr4:55188790..55189653-chr4:55306542..55307230,3	MCF-7	breast:
7	chr4:55188990..55189633-chr4:55827285..55828214,3	K562	blood:
8	chr4:55188935..55189678-chr4:55232967..55233845,2	MCF-7	breast:
9	chr4:55188871..55189578-chr4:55299616..55300145,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000248518	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10016845	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10028483	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029431	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11726309	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11728929	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729535	0.89[ASN][1000 genomes]
rs11732117	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732388	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11737169	0.89[ASN][1000 genomes]
rs1565665	0.84[ASN][1000 genomes]
rs1565668	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17084148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2087806	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28379127	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28714526	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4583821	0.97[ASN][1000 genomes]
rs4864510	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864879	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55836714	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56342025	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57765231	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62299407	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62299416	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6554168	0.84[ASN][1000 genomes]
rs6554170	0.84[ASN][1000 genomes]
rs6850695	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6858442	0.84[ASN][1000 genomes]
rs73234205	0.88[ASN][1000 genomes]
rs9991681	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9994113	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1001094	chr4:55131860-55189739	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv4341	chr4:55172085-55217655	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55183000-55190000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:55188800-55189600	Enhancers	Fetal Brain Male	brain
3	chr4:55189000-55189800	Enhancers	Brain Cingulate Gyrus	brain
4	chr4:55189200-55189800	Enhancers	Brain Substantia Nigra	brain
5	chr4:55189200-55190400	Enhancers	Brain Anterior Caudate	brain
6	chr4:55189400-55189600	Enhancers	Brain Angular Gyrus	brain
7	chr4:55189400-55189800	Enhancers	Brain Hippocampus Middle	brain
8	chr4:55189400-55189800	Enhancers	Brain Inferior Temporal Lobe	brain

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