Variant report

Variant	rs416494
Chromosome Location	chr3:155411663-155411664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10936014	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs173369	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs183088	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs193313	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2015945	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2102897	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2315590	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs358705	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs358729	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs407033	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs410115	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680209	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680210	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680211	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441009	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6769807	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7620748	0.81[AMR][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	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3486322	chr3:155410094-155412301	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv3352105	chr3:155410208-155412306	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2587266	chr3:155410397-155412159	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs416494	PLCH1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155395000-155416800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:155395200-155412000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:155399800-155422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:155400600-155421000	Weak transcription	Fetal Intestine Small	intestine
5	chr3:155400800-155418400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:155408000-155411800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:155408400-155413400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:155408800-155416400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:155408800-155418600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:155409000-155419200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:155409000-155419400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:155409200-155418400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:155409200-155422200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:155411000-155414000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:155411000-155420600	Weak transcription	Fetal Intestine Large	intestine

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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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