Variant report

Variant	rs6777741
Chromosome Location	chr3:155422653-155422654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:155422640-155422712	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PLCH1	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs13076587	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs13079863	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13084995	0.83[ASN][1000 genomes]
rs13089059	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1835212	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]
rs1879090	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1879091	0.91[JPT][hapmap]
rs1879092	0.82[ASN][1000 genomes]
rs2222275	0.85[JPT][hapmap]
rs2435194	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs34810038	0.84[ASN][1000 genomes]
rs358704	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs358706	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs358707	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs358708	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs358710	0.81[CHB][hapmap]
rs358711	0.85[CHB][hapmap]
rs358712	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs358727	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs358896	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs358898	0.83[ASN][1000 genomes]
rs358899	0.90[JPT][hapmap]
rs358902	0.90[JPT][hapmap]
rs358903	0.90[JPT][hapmap]
rs358905	0.90[JPT][hapmap]
rs358910	0.83[ASN][1000 genomes]
rs358911	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs358912	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs378905	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs386867	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs392521	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs394419	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs402201	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs407212	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4083041	0.83[ASN][1000 genomes]
rs412664	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs414126	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs417877	0.85[ASN][1000 genomes]
rs426069	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs430008	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs446716	0.81[JPT][hapmap]
rs448062	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6441006	0.83[ASN][1000 genomes]
rs7428196	0.86[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7645831	0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6777741	SLC33A1	cis	Artery Tibial	GTEx

Chromatin state (count:41 , 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	chr3:155420200-155422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:155420200-155432200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:155420600-155423000	Enhancers	Brain Germinal Matrix	brain
10	chr3:155420800-155423000	Enhancers	Fetal Brain Male	brain
11	chr3:155421200-155423000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:155421400-155423200	Enhancers	Brain Hippocampus Middle	brain
13	chr3:155421400-155423400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:155421600-155422800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:155421600-155423000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:155421600-155423000	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:155421600-155423400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:155421600-155423400	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr3:155421600-155423800	Enhancers	HMEC	breast
20	chr3:155421800-155422800	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr3:155421800-155423400	Enhancers	Brain Angular Gyrus	brain
22	chr3:155421800-155423800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:155422000-155423200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:155422000-155423200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:155422200-155423000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr3:155422200-155423200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:155422200-155423400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:155422200-155423400	Enhancers	Brain Substantia Nigra	brain
29	chr3:155422200-155423600	Enhancers	HepG2	liver
30	chr3:155422200-155427800	Weak transcription	Fetal Intestine Small	intestine
31	chr3:155422400-155422800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:155422400-155422800	Enhancers	H9 Cell Line	embryonic stem cell
33	chr3:155422400-155422800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:155422400-155423200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr3:155422400-155423200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:155422400-155423200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr3:155422400-155423400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:155422400-155423400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:155422400-155423400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:155422600-155422800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:155422600-155423000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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