Variant report

Variant	rs358741
Chromosome Location	chr3:155465932-155465933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 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
2	POLR2A	chr3:155465628-155466090	H1-neurons	neurons:	n/a	n/a
3	KAP1	chr3:155465596-155467159	HEK293	kidney:	n/a	n/a
4	MAFK	chr3:155465886-155466167	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:155465681-155466137	H1-neurons	neurons:	n/a	n/a

No data

(count:4 , 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:

No data

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

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10936015	0.80[AMR][1000 genomes]
rs11923772	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13060077	0.86[CHB][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs173370	0.81[AMR][1000 genomes]
rs17349784	0.86[CHB][hapmap];0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs184836	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2201932	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2315589	0.83[LWK][hapmap]
rs2320190	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35769564	0.80[AFR][1000 genomes]
rs358714	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs358720	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs358722	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs358734	0.83[JPT][hapmap]
rs358736	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs358738	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs358740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs358744	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358745	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358746	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs358748	0.82[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35963081	0.80[AFR][1000 genomes]
rs369155	0.84[ASN][1000 genomes]
rs396797	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs400999	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs426236	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4680215	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680216	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs57183957	0.88[ASN][1000 genomes]
rs62284707	0.87[ASN][1000 genomes]
rs6441012	0.82[ASN][1000 genomes]
rs6774542	0.89[LWK][hapmap];0.83[MKK][hapmap];0.80[AFR][1000 genomes]
rs7619505	0.81[AMR][1000 genomes]
rs7642920	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9866823	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv526490	chr3:155465932-155467069	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs358741	PLCH1	cis	cerebellum	SCAN
rs358741	SLC33A1	cis	parietal	SCAN
rs358741	SLC33A1	cis	cerebellum	SCAN
rs358741	SMC4	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	chr3:155463800-155475200	Weak transcription	Left Ventricle	heart
6	chr3:155463800-155487800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:155463800-155501200	Weak transcription	Aorta	Aorta
8	chr3:155464000-155466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:155464000-155466200	Enhancers	A549	lung
10	chr3:155464000-155476600	Weak transcription	Ovary	ovary
11	chr3:155464200-155466000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:155464200-155466200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:155464200-155466600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:155464200-155469800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:155464200-155474800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:155464200-155487600	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:155464200-155487600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:155464200-155487800	Weak transcription	Adipose Nuclei	Adipose
19	chr3:155464200-155487800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:155464200-155487800	Weak transcription	Pancreas	Pancrea
21	chr3:155464200-155489600	Weak transcription	Brain Anterior Caudate	brain
22	chr3:155464200-155490600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:155464400-155466400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:155464400-155466400	Enhancers	HepG2	liver
25	chr3:155464400-155467200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:155464400-155467400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:155464400-155467400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:155464600-155467200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr3:155464600-155467400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:155464600-155467400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:155464600-155487800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:155465000-155467400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:155465000-155468200	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr3:155465200-155466000	Bivalent Enhancer	Fetal Kidney	kidney
35	chr3:155465200-155466200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:155465200-155466800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:155465200-155467000	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr3:155465400-155466400	Enhancers	Fetal Brain Male	brain
39	chr3:155465400-155468000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr3:155465600-155466000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:155465600-155466200	Enhancers	Brain Germinal Matrix	brain
42	chr3:155465600-155467000	Enhancers	Fetal Brain Female	brain
43	chr3:155465600-155467400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:155465800-155467200	Enhancers	H9 Cell Line	embryonic stem cell
45	chr3:155465800-155467200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:155465800-155468000	Enhancers	HUES64 Cell Line	embryonic stem cell

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