Variant report

Variant	rs35550109
Chromosome Location	chr4:62462234-62462235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10004368	0.86[JPT][hapmap];0.91[MEX][hapmap]
rs10007185	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10018746	0.82[ASW][hapmap];0.86[CEU][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap]
rs10023817	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10866123	0.95[EUR][1000 genomes]
rs11131331	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11131333	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11131337	0.85[JPT][hapmap]
rs11131340	0.91[JPT][hapmap]
rs11931258	0.91[JPT][hapmap]
rs11941524	0.92[EUR][1000 genomes]
rs12233859	0.81[JPT][hapmap]
rs12507326	0.81[JPT][hapmap]
rs12642037	0.91[JPT][hapmap];0.83[MEX][hapmap]
rs12642315	0.84[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12715703	0.85[EUR][1000 genomes]
rs1497897	0.81[JPT][hapmap]
rs1542834	0.81[JPT][hapmap]
rs1846161	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1948616	0.87[MEX][hapmap]
rs2036199	0.91[JPT][hapmap]
rs2172802	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]
rs4860422	0.81[JPT][hapmap]
rs6551636	0.86[JPT][hapmap]
rs7675385	0.89[JPT][hapmap]
rs7690118	0.85[JPT][hapmap]
rs7690595	0.88[EUR][1000 genomes]
rs9991244	0.85[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35550109	LPHN3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62451200-62465000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:62460400-62473400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr4:62461200-62478000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:62461600-62473600	Weak transcription	Fetal Stomach	stomach

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