Variant report

Variant	rs9535780
Chromosome Location	chr13:52448303-52448304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52437942..52440690-chr13:52447041..52448919,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1748124	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17601275	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1886322	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4310756	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4375566	0.83[ASN][1000 genomes]
rs489975	0.81[AMR][1000 genomes]
rs7325195	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7326982	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7350659	0.81[ASN][1000 genomes]
rs7490241	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932914	0.84[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526802	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526803	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535776	0.84[CEU][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs9535779	0.96[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs9535781	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535782	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535783	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535786	0.91[EUR][1000 genomes]
rs9596596	0.85[JPT][hapmap]
rs9596598	0.86[JPT][hapmap]
rs9596607	0.81[AMR][1000 genomes]
rs9634848	0.86[EUR][1000 genomes];0.96[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	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9535780	NEK3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52433800-52479400	Weak transcription	HepG2	liver
2	chr13:52438200-52455400	Weak transcription	Fetal Intestine Small	intestine
3	chr13:52446200-52457000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:52446800-52448400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:52447000-52448800	Enhancers	HSMMtube	muscle
6	chr13:52447200-52448600	Weak transcription	Brain Anterior Caudate	brain
7	chr13:52447800-52448800	Weak transcription	Fetal Kidney	kidney
8	chr13:52447800-52449000	Enhancers	Fetal Thymus	thymus
9	chr13:52448000-52450000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr13:52448200-52448400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr13:52448200-52448600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:52448200-52448600	Enhancers	Brain Germinal Matrix	brain
13	chr13:52448200-52448800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:52448200-52448800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr13:52448200-52448800	Enhancers	Fetal Brain Male	brain
16	chr13:52448200-52448800	Enhancers	Fetal Brain Female	brain
17	chr13:52448200-52449400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr13:52448200-52457000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links