Variant report

Variant	rs1835212
Chromosome Location	chr3:155423302-155423303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs13076587	0.85[JPT][hapmap]
rs13079863	0.89[JPT][hapmap]
rs13089059	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs1879090	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs1879091	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2222275	0.81[JPT][hapmap]
rs358704	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs358706	0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs358707	0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs358708	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs358712	0.81[GIH][hapmap]
rs358726	0.83[MEX][hapmap]
rs358727	0.91[JPT][hapmap]
rs358896	0.85[JPT][hapmap]
rs358897	0.82[ASN][1000 genomes]
rs358899	0.81[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs358902	0.83[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs358903	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs358904	0.81[ASN][1000 genomes]
rs358905	0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs358906	0.82[ASN][1000 genomes]
rs358911	0.86[JPT][hapmap]
rs358912	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs378905	0.81[GIH][hapmap]
rs386867	0.86[JPT][hapmap]
rs392521	0.81[GIH][hapmap]
rs394419	0.81[GIH][hapmap]
rs402201	0.85[CHB][hapmap]
rs407212	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs412664	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs414126	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs426069	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs430008	0.81[GIH][hapmap]
rs6777741	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67955071	0.81[ASN][1000 genomes]
rs7428196	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7645831	0.82[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1835212	SLC33A1	cis	parietal	SCAN
rs1835212	SLC33A1	cis	cerebellum	SCAN
rs1835212	SLC33A1	cis	Artery Tibial	GTEx
rs1835212	PLCH1	cis	cerebellum	SCAN

Chromatin state (count:27 , 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	chr3:155418800-155423400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:155418800-155423400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:155419200-155423600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:155420000-155423800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:155420200-155432200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:155421400-155423400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:155421600-155423400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:155421600-155423400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:155421600-155423800	Enhancers	HMEC	breast
12	chr3:155421800-155423400	Enhancers	Brain Angular Gyrus	brain
13	chr3:155421800-155423800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:155422200-155423400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:155422200-155423400	Enhancers	Brain Substantia Nigra	brain
16	chr3:155422200-155423600	Enhancers	HepG2	liver
17	chr3:155422200-155427800	Weak transcription	Fetal Intestine Small	intestine
18	chr3:155422400-155423400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:155422400-155423400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:155422400-155423400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:155422800-155423400	Enhancers	Brain Anterior Caudate	brain
22	chr3:155423000-155423400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:155423000-155431200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:155423200-155430200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:155423200-155431400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:155423200-155431400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:155423200-155432200	Weak transcription	H1 Cell Line	embryonic stem cell

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