Variant report

Variant	rs3103069
Chromosome Location	chr4:8509451-8509452
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10461079	0.89[EUR][1000 genomes]
rs1357481	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543246	0.97[ASN][1000 genomes]
rs1880023	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880024	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1916326	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1949733	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2010758	0.89[ASN][1000 genomes]
rs2140337	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255501	0.83[EUR][1000 genomes]
rs2386227	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2450475	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2631731	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2631734	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2631736	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2631740	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631742	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631743	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631744	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631745	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631746	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631754	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2631756	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2631758	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2631762	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2688219	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2688223	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688227	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2688231	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2688233	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688235	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2688242	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2688243	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2688247	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3103067	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3103070	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3103071	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3103072	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3103099	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696828	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6447875	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6837429	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6858542	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868105	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs871768	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs940133	0.95[EUR][1000 genomes]
rs940134	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs940136	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv4224	chr4:8503727-8546462	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3327752	chr4:8507302-8509800	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3103069	ACOX3	Cis_1M	lymphoblastoid	RTeQTL
rs3103069	RP11-689P11.2	cis	lung	GTEx
rs3103069	TRMT44	cis	Nerve Tibial	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8501800-8510600	Enhancers	Ovary	ovary
2	chr4:8502800-8512800	Enhancers	Placenta	Placenta
3	chr4:8503600-8509800	Enhancers	Adipose Nuclei	Adipose
4	chr4:8504200-8510600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:8504600-8510800	Enhancers	Fetal Muscle Leg	muscle
6	chr4:8505800-8509600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:8505800-8509800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:8506200-8509600	Enhancers	HSMMtube	muscle
9	chr4:8507000-8509800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr4:8507200-8512000	Weak transcription	Gastric	stomach
11	chr4:8507600-8509600	Enhancers	Colon Smooth Muscle	Colon
12	chr4:8507800-8509600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:8507800-8509600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:8507800-8509600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr4:8507800-8509600	Enhancers	HSMM	muscle
16	chr4:8507800-8509800	Enhancers	Rectal Smooth Muscle	rectum
17	chr4:8507800-8510000	Enhancers	NHDF-Ad	bronchial
18	chr4:8508000-8509600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr4:8508000-8509600	Enhancers	NHLF	lung
20	chr4:8508200-8509600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr4:8508200-8511600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:8508400-8510400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:8508800-8509600	Enhancers	Osteobl	bone
24	chr4:8509000-8509600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:8509000-8509800	Enhancers	Fetal Muscle Trunk	muscle
26	chr4:8509000-8510000	Weak transcription	Spleen	Spleen
27	chr4:8509000-8519200	Weak transcription	Brain Germinal Matrix	brain
28	chr4:8509200-8509600	Enhancers	Stomach Smooth Muscle	stomach
29	chr4:8509200-8511200	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:8509200-8513200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:8509400-8509600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:8509400-8509800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:8509400-8510400	Weak transcription	Brain Anterior Caudate	brain
34	chr4:8509400-8513200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:8509400-8514000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:8509400-8517200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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