Variant report

Variant	rs358742
Chromosome Location	chr3:155465491-155465492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr3:155465273-155466975	U2OS	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:155460020..155464783-chr3:155465201..155469112,6	K562	blood:
2	chr3:155465236..155465956-chr9:98268514..98269039,2	NB4	blood:
3	chr3:155461411..155464910-chr3:155465071..155468362,4	MCF-7	breast:
4	chr3:155461079..155463376-chr3:155465033..155467779,3	MCF-7	breast:
5	chr3:155461486..155465793-chr3:155586998..155592801,6	K562	blood:

No data

Variant related genes	Relation type
PLCH1	TF binding region
ENSG00000214919	TF binding region
ENSG00000214919	Chromatin interaction
ENSG00000114805	Chromatin interaction
ENSG00000271155	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000163655	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12486921	0.89[EUR][1000 genomes]
rs13089059	0.84[MEX][hapmap]
rs1879090	0.89[MEX][hapmap]
rs2222275	0.84[MEX][hapmap]
rs358713	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs358721	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs358724	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs358725	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs358727	0.83[MEX][hapmap]
rs358728	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs358732	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs358737	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358739	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs358747	0.95[ASN][1000 genomes]
rs358749	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs358903	0.84[MEX][hapmap]
rs358911	0.84[MEX][hapmap]
rs358912	0.84[MEX][hapmap]
rs359545	0.89[MEX][hapmap]
rs395667	0.89[EUR][1000 genomes]
rs404570	0.83[CHD][hapmap]
rs427139	0.89[EUR][1000 genomes]
rs492858	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs500347	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62284741	0.89[EUR][1000 genomes]
rs7650414	0.84[ASN][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	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
3	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv521244	chr3:155465491-155467069	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs358742	PLCH1	cis	cerebellum	SCAN
rs358742	SMC4	cis	cerebellum	SCAN
rs358742	C3orf33	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155462800-155466600	Weak transcription	Hela-S3	cervix
2	chr3:155463200-155466200	Weak transcription	K562	blood
3	chr3:155463200-155466600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:155463200-155467400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:155463400-155465800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:155463800-155475200	Weak transcription	Left Ventricle	heart
7	chr3:155463800-155487800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:155463800-155501200	Weak transcription	Aorta	Aorta
9	chr3:155464000-155466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:155464000-155466200	Enhancers	A549	lung
11	chr3:155464000-155476600	Weak transcription	Ovary	ovary
12	chr3:155464200-155465600	Weak transcription	Brain Germinal Matrix	brain
13	chr3:155464200-155465600	Weak transcription	Fetal Brain Female	brain
14	chr3:155464200-155465800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:155464200-155466000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr3:155464200-155466200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:155464200-155466600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:155464200-155469800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:155464200-155474800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:155464200-155487600	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:155464200-155487600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:155464200-155487800	Weak transcription	Adipose Nuclei	Adipose
23	chr3:155464200-155487800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:155464200-155487800	Weak transcription	Pancreas	Pancrea
25	chr3:155464200-155489600	Weak transcription	Brain Anterior Caudate	brain
26	chr3:155464200-155490600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:155464400-155465600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:155464400-155466400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:155464400-155466400	Enhancers	HepG2	liver
30	chr3:155464400-155467200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:155464400-155467400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:155464400-155467400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr3:155464600-155467200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr3:155464600-155467400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:155464600-155467400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr3:155464600-155487800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:155465000-155465600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:155465000-155467400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:155465000-155468200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr3:155465200-155466000	Bivalent Enhancer	Fetal Kidney	kidney
41	chr3:155465200-155466200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:155465200-155466800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:155465200-155467000	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr3:155465400-155465800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:155465400-155466400	Enhancers	Fetal Brain Male	brain
46	chr3:155465400-155468000	Enhancers	H1 Cell Line	embryonic stem cell

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