Variant report

Variant	rs358748
Chromosome Location	chr3:155457386-155457387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155449822..155451329-chr3:155456131..155457653,2	K562	blood:
2	chr3:155457303..155459109-chr3:155460905..155462872,3	MCF-7	breast:
3	chr3:155457065..155458861-chr3:155462377..155464396,2	K562	blood:

Variant related genes	Relation type
ENSG00000214919	Chromatin interaction
ENSG00000114805	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10936015	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11923772	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs173370	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs181588	0.80[EUR][1000 genomes]
rs184836	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2320190	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358714	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358720	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358722	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs358734	0.83[JPT][hapmap]
rs358736	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs358738	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358740	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs358741	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]
rs358744	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs358745	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs358746	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs369155	0.81[ASN][1000 genomes]
rs396797	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs400999	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs426236	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4680215	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680216	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs57183957	0.84[ASN][1000 genomes]
rs62284707	0.84[ASN][1000 genomes]
rs7619505	0.82[AMR][1000 genomes]
rs9866823	0.82[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
rs358748	SLC33A1	cis	cerebellum	SCAN
rs358748	PLCH1	cis	cerebellum	SCAN
rs358748	SLC33A1	cis	parietal	SCAN

Chromatin state (count:32 , 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	chr3:155455800-155461400	Weak transcription	Brain Substantia Nigra	brain
8	chr3:155455800-155461400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:155456000-155460200	Weak transcription	Brain Anterior Caudate	brain
10	chr3:155456000-155461400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:155456200-155458800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:155456200-155461200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:155456200-155461400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:155456200-155461400	Weak transcription	K562	blood
15	chr3:155456200-155461600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:155456400-155458200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:155456400-155461400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:155456600-155457400	Flanking Active TSS	HepG2	liver
19	chr3:155456600-155457600	Enhancers	Fetal Intestine Small	intestine
20	chr3:155456600-155457600	Flanking Active TSS	A549	lung
21	chr3:155456800-155457400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:155456800-155457400	Enhancers	Fetal Lung	lung
23	chr3:155456800-155457600	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:155456800-155457600	Enhancers	Duodenum Mucosa	Duodenum
25	chr3:155456800-155457600	Enhancers	Fetal Kidney	kidney
26	chr3:155456800-155461400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:155457000-155457400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:155457000-155457400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:155457000-155457600	Weak transcription	Colonic Mucosa	Colon
30	chr3:155457000-155459200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:155457000-155461000	Weak transcription	Fetal Intestine Large	intestine
32	chr3:155457200-155457600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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