Variant report

Variant	rs3115396
Chromosome Location	chr4:8510952-8510953
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8460137..8461781-chr4:8510827..8513622,2	K562	blood:
2	chr4:8510207..8512745-chr4:8513756..8515974,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METTL19-1	chr4:8510525-8511526	ENSG00000205959.3

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11729265	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12503034	0.86[EUR][1000 genomes]
rs1880025	0.87[EUR][1000 genomes]
rs2002860	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2245515	0.89[EUR][1000 genomes]
rs2245808	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2386223	0.85[EUR][1000 genomes]
rs2631723	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2631724	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2631727	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2631728	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2631729	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2631730	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2631733	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2631737	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2631757	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2631764	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2631769	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688221	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2688228	0.88[EUR][1000 genomes]
rs2688229	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2688230	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2688234	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2688239	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2688240	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3103090	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3103098	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4325994	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56343159	0.91[EUR][1000 genomes]
rs954271	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3115396	RP11-774O3.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8502800-8512800	Enhancers	Placenta	Placenta
2	chr4:8507200-8512000	Weak transcription	Gastric	stomach
3	chr4:8508200-8511600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:8509000-8519200	Weak transcription	Brain Germinal Matrix	brain
5	chr4:8509200-8511200	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:8509200-8513200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:8509400-8513200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:8509400-8514000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:8509400-8517200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:8509600-8514200	Weak transcription	HSMMtube	muscle
11	chr4:8509600-8515200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:8509600-8515600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:8509800-8511600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr4:8510000-8515600	Weak transcription	NHDF-Ad	bronchial
15	chr4:8510400-8512200	ZNF genes & repeats	Spleen	Spleen
16	chr4:8510800-8511000	Weak transcription	Fetal Muscle Leg	muscle

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