Variant report

Variant	rs1109911
Chromosome Location	chr5:124485345-124485346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-43D2.2.1-13	chr5:124485221-124485622	ENSG00000249365

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10040497	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10050592	0.88[EUR][1000 genomes]
rs10050742	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10051335	0.83[ASN][1000 genomes]
rs10067150	0.96[ASN][1000 genomes]
rs10067228	0.96[ASN][1000 genomes]
rs10068672	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085148	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1008776	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1109910	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1109912	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241788	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11241789	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11741331	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11743350	0.96[ASN][1000 genomes]
rs11744843	0.96[ASN][1000 genomes]
rs11746972	0.96[ASN][1000 genomes]
rs11747137	0.96[ASN][1000 genomes]
rs12188105	0.91[ASN][1000 genomes]
rs12189383	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12520570	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13161894	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13162105	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162223	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13178008	0.91[ASN][1000 genomes]
rs13187207	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13188430	0.91[ASN][1000 genomes]
rs13359280	0.96[ASN][1000 genomes]
rs1371373	0.96[ASN][1000 genomes]
rs1371374	0.96[ASN][1000 genomes]
rs1550356	0.91[ASN][1000 genomes]
rs1550357	0.91[ASN][1000 genomes]
rs1550358	0.91[ASN][1000 genomes]
rs1550361	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1550364	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1550365	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17449514	0.83[ASN][1000 genomes]
rs17456443	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17456490	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033842	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2218125	0.87[ASN][1000 genomes]
rs28662294	0.91[ASN][1000 genomes]
rs34348381	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34519250	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35918516	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4836151	0.91[ASN][1000 genomes]
rs4836153	0.91[ASN][1000 genomes]
rs4836155	0.91[ASN][1000 genomes]
rs5016080	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5016082	0.96[ASN][1000 genomes]
rs5016083	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065010	0.83[ASN][1000 genomes]
rs56171860	0.87[ASN][1000 genomes]
rs61581106	0.96[ASN][1000 genomes]
rs62375663	0.96[ASN][1000 genomes]
rs62375664	0.96[ASN][1000 genomes]
rs6595576	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595577	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595578	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862170	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865099	0.87[ASN][1000 genomes]
rs6865632	0.87[ASN][1000 genomes]
rs6869646	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6885185	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6886317	0.87[ASN][1000 genomes]
rs6888003	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6892666	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719958	0.96[ASN][1000 genomes]
rs7720525	0.96[ASN][1000 genomes]
rs7721241	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7724689	0.96[ASN][1000 genomes]
rs7733868	0.87[ASN][1000 genomes]
rs953844	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9686650	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830475	chr5:124387292-124550256	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv599658	chr5:124459547-124513012	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124477200-124488200	Weak transcription	HUVEC	blood vessel
2	chr5:124484000-124490800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:124484200-124485400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:124484200-124485400	Enhancers	NHDF-Ad	bronchial
5	chr5:124484200-124486400	Enhancers	Fetal Stomach	stomach
6	chr5:124484400-124486000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:124484800-124485400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:124484800-124485400	Enhancers	Brain Hippocampus Middle	brain
9	chr5:124484800-124485400	Enhancers	Small Intestine	intestine
10	chr5:124484800-124485600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:124484800-124485600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:124484800-124486000	Weak transcription	Adipose Nuclei	Adipose
13	chr5:124484800-124487200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr5:124485000-124485400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr5:124485000-124485600	Enhancers	Fetal Muscle Leg	muscle
16	chr5:124485000-124490000	Enhancers	Fetal Lung	lung
17	chr5:124485200-124485400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr5:124485200-124485400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:124485200-124485400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr5:124485200-124485600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:124485200-124486000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr5:124485200-124486000	Enhancers	HSMMtube	muscle
23	chr5:124485200-124486800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:124485200-124487800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:124485200-124488800	Enhancers	Brain Substantia Nigra	brain
26	chr5:124485200-124490000	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links