Variant report

Variant	rs10474346
Chromosome Location	chr5:90564139-90564140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90559982..90565400-chr5:90570467..90573729,4	K562	blood:
2	chr5:90555805..90566288-chr5:90673548..90682139,22	K562	blood:
3	chr5:90562352..90564366-chr5:90565148..90567922,2	K562	blood:
4	chr5:90560937..90569122-chr5:90675177..90680484,12	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction
ENSG00000199643	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10038090	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10061355	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10462343	0.92[ASN][1000 genomes]
rs10462492	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs10474347	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs12697807	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs13171635	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1511344	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1511345	0.83[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1543066	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1858309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2048451	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs2048452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973441	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4019243	0.84[ASN][1000 genomes]
rs4019302	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4364415	0.97[ASN][1000 genomes]
rs4377733	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4424024	0.92[ASN][1000 genomes]
rs4518439	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859170	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6869552	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6882172	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6885341	0.97[ASN][1000 genomes]
rs6888389	0.95[ASN][1000 genomes]
rs6888674	0.95[ASN][1000 genomes]
rs6889197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6897578	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6898622	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7709572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7719516	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs7724489	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90561000-90564800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:90562200-90564400	Weak transcription	Thymus	Thymus
3	chr5:90562200-90564600	Weak transcription	K562	blood
4	chr5:90562400-90564600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:90562400-90564600	Weak transcription	HMEC	breast
6	chr5:90562600-90564600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:90562600-90564600	Weak transcription	Primary T cells from cord blood	blood
8	chr5:90562600-90564600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:90562600-90564600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:90562600-90573200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:90562800-90564600	Weak transcription	GM12878-XiMat	blood
12	chr5:90562800-90564800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:90562800-90568000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:90562800-90568600	Weak transcription	Hela-S3	cervix
15	chr5:90562800-90568800	Weak transcription	Fetal Heart	heart

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