Variant report

Variant	rs1044352
Chromosome Location	chr4:31147874-31147875
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:31145390..31148497-chr4:31150587..31153361,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10030161	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1044353	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463845	0.86[ASN][1000 genomes]
rs1463846	0.88[ASN][1000 genomes]
rs1463847	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463848	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463849	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1499476	0.82[EUR][1000 genomes]
rs16884451	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884471	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884473	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1846526	0.83[EUR][1000 genomes]
rs28483036	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28498976	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4692500	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448743	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6448744	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6818974	0.88[ASN][1000 genomes]
rs6820584	0.83[EUR][1000 genomes]
rs7655744	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671046	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674487	0.82[EUR][1000 genomes]
rs7674790	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7686226	0.87[ASN][1000 genomes]
rs952617	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998450	chr4:30823631-31628179	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1007884	chr4:31071934-31680623	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007145	chr4:31079681-31670541	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv491749	chr4:31103307-31645668	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Epilepsy	25087078	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1044352	PCDH7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:31142000-31149600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:31142600-31150000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:31143000-31150400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:31143000-31151800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:31145600-31154400	Weak transcription	Fetal Heart	heart
6	chr4:31146200-31148000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:31146600-31150400	Weak transcription	Fetal Lung	lung
8	chr4:31147000-31148600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:31147000-31150400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:31147400-31148800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr4:31147600-31148200	Enhancers	Fetal Intestine Small	intestine
12	chr4:31147600-31148600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:31147800-31148200	Weak transcription	Stomach Mucosa	stomach
14	chr4:31147800-31148600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr4:31147800-31150600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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