Variant report

Variant	rs3733083
Chromosome Location	chr3:53925170-53925171
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
2	chr3:53924684..53925501-chr7:135346877..135347648,2	NB4	blood:
3	chr19:1268912..1269727-chr3:53925139..53925887,2	Hela-S3	cervix:
4	chr3:53909521..53911477-chr3:53924349..53927028,2	MCF-7	breast:
5	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
6	chr3:53921644..53923214-chr3:53923445..53925751,2	MCF-7	breast:
7	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099622	Chromatin interaction
ENSG00000243317	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000222888	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1020082	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1134091	0.89[EUR][1000 genomes]
rs12632292	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17053568	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17053590	0.91[EUR][1000 genomes]
rs1982171	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241806	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2276840	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276843	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276844	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276845	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289203	0.91[EUR][1000 genomes]
rs2304575	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304576	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2884631	0.86[EUR][1000 genomes]
rs3017	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733075	0.85[EUR][1000 genomes]
rs3733079	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821868	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821869	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41292476	0.87[EUR][1000 genomes]
rs4141606	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs45511795	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687594	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4687753	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687756	0.91[EUR][1000 genomes]
rs4687758	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687760	0.87[EUR][1000 genomes]
rs55917919	0.92[EUR][1000 genomes]
rs56743403	0.91[EUR][1000 genomes]
rs57398949	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62253003	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62253004	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6445612	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs709324	0.86[EUR][1000 genomes]
rs73078007	0.84[EUR][1000 genomes]
rs9840445	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9849951	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9850063	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9860367	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880056	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs999515	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3733083	ACTR8	cis	Thyroid	GTEx
rs3733083	SELK	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53919600-53925200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:53923400-53926400	Active TSS	Right Ventricle	heart
3	chr3:53923600-53926600	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr3:53924000-53925200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:53924000-53925200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:53924000-53925200	Flanking Active TSS	Liver	Liver
7	chr3:53924000-53925200	Flanking Active TSS	Brain Germinal Matrix	brain
8	chr3:53924000-53925200	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr3:53924000-53925200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr3:53924000-53925200	Enhancers	Spleen	Spleen
11	chr3:53924000-53925200	Flanking Active TSS	Hela-S3	cervix
12	chr3:53924000-53925400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:53924000-53925400	Flanking Active TSS	Brain Angular Gyrus	brain
14	chr3:53924000-53926400	Active TSS	Colonic Mucosa	Colon
15	chr3:53924200-53925200	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr3:53924200-53925200	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr3:53924200-53925200	Flanking Active TSS	Colon Smooth Muscle	Colon
18	chr3:53924200-53925200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr3:53924200-53925200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr3:53924200-53925200	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr3:53924200-53925200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr3:53924200-53926600	Active TSS	Psoas Muscle	Psoas
23	chr3:53924200-53926600	Active TSS	Right Atrium	heart
24	chr3:53924200-53926800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:53924400-53925200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:53924400-53925200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:53924400-53925200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:53924400-53925200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr3:53924400-53925200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr3:53924400-53925200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr3:53924400-53925200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:53924400-53925200	Flanking Active TSS	Fetal Kidney	kidney
33	chr3:53924400-53925400	Flanking Active TSS	Osteobl	bone
34	chr3:53924400-53926400	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr3:53924400-53926400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:53924400-53926800	Active TSS	HSMMtube	muscle
37	chr3:53924600-53925200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:53924600-53925200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:53924600-53925200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:53924600-53925200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr3:53924600-53925200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:53924600-53925200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:53924600-53925200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr3:53924600-53925200	Flanking Active TSS	Fetal Brain Male	brain
45	chr3:53924600-53925200	Flanking Active TSS	Fetal Heart	heart
46	chr3:53924600-53925200	Flanking Active TSS	Fetal Lung	lung
47	chr3:53924600-53925200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr3:53924600-53925200	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr3:53924600-53925400	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr3:53924600-53925400	Flanking Active TSS	Primary hematopoietic stem cells	blood

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