Variant report

Variant	rs4838428
Chromosome Location	chr10:49832239-49832240
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC18-3	chr10:49832049-49832477	ENSG00000251413.1

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10776629	0.91[EUR][1000 genomes]
rs10776630	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10776631	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10776632	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857612	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10857613	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857614	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1822861	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2377522	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2377523	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2377596	0.81[AMR][1000 genomes]
rs34939981	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3844493	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3845284	0.85[EUR][1000 genomes]
rs3853123	0.91[EUR][1000 genomes]
rs3910909	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3910910	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3910911	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4838429	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7904633	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4838428	ARHGAP22	cis	Whole Blood	GTEx
rs4838428	ARHGAP22	cis	Artery Aorta	GTEx
rs4838428	ARHGAP22	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49813400-49844200	Weak transcription	Pancreas	Pancrea
2	chr10:49828800-49841400	Weak transcription	Aorta	Aorta
3	chr10:49831000-49832400	Bivalent Enhancer	Primary B cells from cord blood	blood
4	chr10:49831000-49833600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr10:49831000-49834400	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:49831000-49835800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:49831200-49832400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr10:49831200-49832400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:49831200-49832600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:49831200-49834200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:49831400-49832400	Weak transcription	Spleen	Spleen
12	chr10:49831400-49835600	Enhancers	HUVEC	blood vessel
13	chr10:49831600-49833600	Enhancers	Osteobl	bone
14	chr10:49831600-49833800	Enhancers	NHDF-Ad	bronchial
15	chr10:49831600-49834600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:49831600-49843400	Weak transcription	Right Atrium	heart
17	chr10:49831800-49835000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr10:49832000-49832800	Weak transcription	NH-A	brain
19	chr10:49832000-49833200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:49832000-49833400	Weak transcription	GM12878-XiMat	blood
21	chr10:49832000-49834200	Enhancers	NHLF	lung
22	chr10:49832200-49832400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:49832200-49832400	Enhancers	Brain Substantia Nigra	brain
24	chr10:49832200-49834000	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links