Variant report

Variant	rs904243
Chromosome Location	chr4:62406445-62406446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1391321	1.00[ASW][hapmap];0.83[LWK][hapmap]
rs1603147	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958862	0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv2753138	chr4:62271444-62442507	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs904243	LPHN3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62397000-62406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:62404800-62406800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:62404800-62408000	Enhancers	Fetal Intestine Small	intestine
4	chr4:62405400-62408400	Enhancers	Fetal Intestine Large	intestine
5	chr4:62405600-62406800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:62406000-62407600	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr4:62406200-62406800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:62406200-62407600	Enhancers	Fetal Heart	heart
9	chr4:62406400-62406800	Weak transcription	Stomach Mucosa	stomach
10	chr4:62406400-62407000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr4:62406400-62407000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr4:62406400-62407400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:62406400-62407400	Enhancers	Duodenum Mucosa	Duodenum
14	chr4:62406400-62407600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr4:62406400-62408000	Enhancers	Rectal Mucosa Donor 31	rectum

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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