Variant report

Variant	rs3103099
Chromosome Location	chr4:8511567-8511568
allele	C/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:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10461079	0.88[EUR][1000 genomes]
rs1357481	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1543246	0.94[ASN][1000 genomes]
rs1880023	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1880024	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1916326	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1949733	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2010758	0.85[ASN][1000 genomes]
rs2140337	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255501	0.82[EUR][1000 genomes]
rs2386227	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2450475	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631731	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2631734	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2631736	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2631740	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2631742	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631743	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631744	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631745	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631746	0.91[ASN][1000 genomes]
rs2631754	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2631756	0.85[AMR][1000 genomes]
rs2631758	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631762	0.85[AMR][1000 genomes]
rs2688219	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2688223	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2688227	0.85[AMR][1000 genomes]
rs2688231	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2688233	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2688235	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2688242	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2688243	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2688247	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3103067	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3103069	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3103070	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3103071	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3103072	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696828	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6447875	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6837429	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6858542	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868105	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs871768	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs940133	0.94[EUR][1000 genomes]
rs940134	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs940136	0.87[AMR][1000 genomes];0.83[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3103099	RP11-689P11.2	cis	lung	GTEx
rs3103099	TRMT44	cis	Nerve Tibial	GTEx
rs3103099	ACOX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 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	chr4:8509200-8513200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:8509400-8513200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:8509400-8514000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:8509400-8517200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:8509600-8514200	Weak transcription	HSMMtube	muscle
10	chr4:8509600-8515200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:8509600-8515600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:8509800-8511600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr4:8510000-8515600	Weak transcription	NHDF-Ad	bronchial
14	chr4:8510400-8512200	ZNF genes & repeats	Spleen	Spleen
15	chr4:8511200-8511600	Enhancers	Brain Hippocampus Middle	brain
16	chr4:8511400-8511600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:8511400-8511600	Enhancers	Right Ventricle	heart

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