Variant report

Variant	rs2172802
Chromosome Location	chr4:62453209-62453210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10007185	0.80[EUR][1000 genomes]
rs10018746	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap]
rs10866123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10866124	0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11131329	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs11131331	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11131333	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11131334	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11941524	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642315	0.89[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12715703	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12715704	0.84[ASN][1000 genomes]
rs1497906	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs1497907	0.81[CHB][hapmap]
rs1603660	0.84[ASN][1000 genomes]
rs17239080	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1846160	0.92[ASN][1000 genomes]
rs35550109	0.82[ASW][hapmap];0.95[CEU][hapmap];0.90[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes]
rs6551634	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7669283	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7690595	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9685140	0.93[ASN][1000 genomes]
rs9991244	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868844	chr4:62241702-62497248	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv461377	chr4:62368762-62883431	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv594328	chr4:62368762-62883431	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1004815	chr4:62398737-62553769	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv537110	chr4:62398737-62553769	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv594329	chr4:62416593-62478230	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv879077	chr4:62419426-62545435	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Partial epilepsies	20522523	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2172802	LPHN3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62446400-62462200	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:62451200-62460600	Weak transcription	Fetal Stomach	stomach
3	chr4:62451200-62465000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:62451400-62460600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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