Variant report

Variant	rs3733079
Chromosome Location	chr3:53911540-53911541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53908420..53912131-chr3:53913956..53917012,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222888	Chromatin interaction
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1020082	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1134091	0.88[EUR][1000 genomes]
rs12632292	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17053568	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17053590	1.00[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1982171	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241806	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2276840	0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276845	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289203	1.00[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2304575	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304576	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2884631	0.86[EUR][1000 genomes]
rs3017	0.81[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733075	0.84[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs3733083	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821868	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821869	0.84[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41292476	0.86[EUR][1000 genomes]
rs4141606	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45511795	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687594	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4687753	0.84[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4687756	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[EUR][1000 genomes]
rs4687758	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687760	0.84[EUR][1000 genomes]
rs55917919	0.89[EUR][1000 genomes]
rs56743403	0.90[EUR][1000 genomes]
rs57398949	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62253003	0.87[ASN][1000 genomes]
rs62253004	0.87[ASN][1000 genomes]
rs6445612	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs709324	0.86[EUR][1000 genomes]
rs73078007	0.81[EUR][1000 genomes]
rs9840445	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9849951	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9850063	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9860367	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880056	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs999515	0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3733079	ACTR8	cis	cerebellum	SCAN
rs3733079	ACTR8	cis	Thyroid	GTEx
rs3733079	SFMBT1	cis	cerebellum	SCAN
rs3733079	PHF7	cis	cerebellum	SCAN
rs3733079	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs3733079	ACTR8	cis	parietal	SCAN
rs3733079	IL17RB	cis	cerebellum	SCAN
rs3733079	ACTR8	cis	lymphoblastoid	seeQTL
rs3733079	IL17RB	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
2	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr3:53891400-53914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:53891800-53912800	Strong transcription	Brain Germinal Matrix	brain
8	chr3:53892000-53914400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:53892200-53912400	Strong transcription	Fetal Brain Female	brain
10	chr3:53892200-53914000	Strong transcription	Adipose Nuclei	Adipose
11	chr3:53892200-53914400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:53892200-53914600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:53892400-53913000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:53892400-53913800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:53892400-53914200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr3:53892400-53914400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:53892600-53914200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:53892600-53914400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:53892600-53914400	Strong transcription	Fetal Muscle Leg	muscle
20	chr3:53892800-53914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:53892800-53914200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:53892800-53914200	Strong transcription	Thymus	Thymus
23	chr3:53892800-53914400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:53892800-53914600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr3:53893000-53914000	Strong transcription	Placenta	Placenta
26	chr3:53893000-53914400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:53893200-53914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:53893200-53914200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:53893200-53914200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:53893200-53914200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:53893200-53914600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:53893400-53914200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:53893800-53912800	Strong transcription	Brain Anterior Caudate	brain
34	chr3:53894200-53914400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:53894400-53914000	Strong transcription	Primary T cells from cord blood	blood
36	chr3:53894400-53914400	Strong transcription	Fetal Thymus	thymus
37	chr3:53894800-53914200	Strong transcription	Primary hematopoietic stem cells	blood
38	chr3:53894800-53914200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:53895000-53914000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:53895000-53914200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:53895000-53914400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:53895200-53913200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:53895200-53914200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr3:53895200-53914200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:53895200-53914200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:53895400-53913800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:53895600-53914200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:53895800-53913800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:53896200-53912800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr3:53896800-53914200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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