Variant report

Variant	rs358749
Chromosome Location	chr3:155457046-155457047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155449822..155451329-chr3:155456131..155457653,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12486921	0.87[EUR][1000 genomes]
rs13089059	0.84[MEX][hapmap]
rs1879090	0.89[MEX][hapmap]
rs2222275	0.84[MEX][hapmap]
rs358713	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs358721	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs358724	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs358725	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs358727	0.83[MEX][hapmap]
rs358728	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs358732	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs358737	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs358739	0.89[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.95[ASN][1000 genomes]
rs358742	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs358747	0.99[ASN][1000 genomes]
rs358903	0.84[MEX][hapmap]
rs358911	0.84[MEX][hapmap]
rs358912	0.84[MEX][hapmap]
rs359545	0.89[MEX][hapmap]
rs395667	0.87[EUR][1000 genomes]
rs427139	0.87[EUR][1000 genomes]
rs492858	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs500347	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs592982	0.84[MEX][hapmap]
rs62284741	0.87[EUR][1000 genomes]
rs7650414	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs358749	PLCH1	cis	cerebellum	SCAN
rs358749	C3orf33	cis	cerebellum	SCAN
rs358749	SMC4	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155432400-155461600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:155449200-155461200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:155449800-155458200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:155454400-155457400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr3:155454400-155458600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:155454600-155458600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:155455800-155457200	Enhancers	Stomach Mucosa	stomach
8	chr3:155455800-155461400	Weak transcription	Brain Substantia Nigra	brain
9	chr3:155455800-155461400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:155456000-155460200	Weak transcription	Brain Anterior Caudate	brain
11	chr3:155456000-155461400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:155456200-155457200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:155456200-155458800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:155456200-155461200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:155456200-155461400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:155456200-155461400	Weak transcription	K562	blood
17	chr3:155456200-155461600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:155456400-155458200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:155456400-155461400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:155456600-155457400	Flanking Active TSS	HepG2	liver
21	chr3:155456600-155457600	Enhancers	Fetal Intestine Small	intestine
22	chr3:155456600-155457600	Flanking Active TSS	A549	lung
23	chr3:155456800-155457400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:155456800-155457400	Enhancers	Fetal Lung	lung
25	chr3:155456800-155457600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:155456800-155457600	Enhancers	Duodenum Mucosa	Duodenum
27	chr3:155456800-155457600	Enhancers	Fetal Kidney	kidney
28	chr3:155456800-155461400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:155457000-155457400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:155457000-155457400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:155457000-155457600	Weak transcription	Colonic Mucosa	Colon
32	chr3:155457000-155459200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:155457000-155461000	Weak transcription	Fetal Intestine Large	intestine

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