Variant report

Variant	rs193313
Chromosome Location	chr3:155425866-155425867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12053896	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs173369	0.89[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs183088	0.89[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2015945	0.86[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2102897	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs358705	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs358726	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs358908	0.86[JPT][hapmap]
rs358909	0.86[JPT][hapmap]
rs407033	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs410115	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs416494	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4680209	0.87[EUR][1000 genomes]
rs4680210	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs4680211	0.87[EUR][1000 genomes]
rs6441009	0.87[EUR][1000 genomes]
rs6768777	0.81[JPT][hapmap]
rs6769807	0.85[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs193313	PLCH1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155412600-155437400	Weak transcription	Pancreas	Pancrea
2	chr3:155413800-155432000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:155420200-155432200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:155422200-155427800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:155423000-155431200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:155423200-155430200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:155423200-155431400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:155423200-155431400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:155423200-155432200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:155423400-155426000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:155423400-155426000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:155423400-155431200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:155423600-155427400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:155423600-155430600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:155423600-155431000	Weak transcription	HepG2	liver

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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