Variant report

Variant	rs6885458
Chromosome Location	chr5:98381752-98381753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98264902..98266916-chr5:98381565..98384690,3	K562	blood:
2	chr5:98380774..98382575-chr5:98387659..98389837,2	K562	blood:
3	chr5:98247883..98250755-chr5:98381007..98383241,2	K562	blood:

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10037147	0.83[EUR][1000 genomes]
rs10038192	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10040066	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10041261	0.94[ASN][1000 genomes]
rs10041263	0.80[AFR][1000 genomes]
rs10041335	0.80[AFR][1000 genomes]
rs10050423	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10054523	0.82[AFR][1000 genomes]
rs10055595	0.80[AFR][1000 genomes]
rs10076291	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10077697	0.82[AFR][1000 genomes]
rs10085106	0.81[AFR][1000 genomes]
rs10085145	0.82[AFR][1000 genomes]
rs10479344	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10479345	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10479346	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10479348	0.92[ASN][1000 genomes]
rs10479350	0.82[AFR][1000 genomes]
rs10479351	0.82[AFR][1000 genomes]
rs10479352	0.82[AFR][1000 genomes]
rs1093794	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1104262	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11242567	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242574	1.00[ASN][1000 genomes]
rs11745405	1.00[ASN][1000 genomes]
rs11949103	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11950452	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11950855	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11960896	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12109067	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189335	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12515042	1.00[ASN][1000 genomes]
rs13179812	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1393210	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472622	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1604450	1.00[ASN][1000 genomes]
rs161731	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs161935	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs161936	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs162341	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17166575	0.80[AFR][1000 genomes]
rs17166578	0.81[AFR][1000 genomes]
rs172874	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1875529	1.00[ASN][1000 genomes]
rs2221268	0.94[ASN][1000 genomes]
rs2455423	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28555343	0.82[AFR][1000 genomes]
rs28656032	0.82[AFR][1000 genomes]
rs2927647	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2927648	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2927654	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2937706	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2937708	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2937709	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs325220	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs326493	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs327807	0.83[EUR][1000 genomes]
rs34489	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34490	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34491	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34496	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34497	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34499	0.85[EUR][1000 genomes]
rs363929	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs366000	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs366353	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs370529	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs378089	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs380156	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs393697	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs395668	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs398436	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40075	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs407562	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs416750	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs422127	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs434039	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4343864	0.90[ASN][1000 genomes]
rs443726	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4448016	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447044	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs449204	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs451141	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4565239	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4583911	1.00[ASN][1000 genomes]
rs45931	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs469018	0.82[EUR][1000 genomes]
rs4703048	0.85[EUR][1000 genomes]
rs4703049	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4703051	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4703052	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4703340	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4703345	0.94[ASN][1000 genomes]
rs539024	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55780476	0.80[AFR][1000 genomes]
rs55821667	0.80[AFR][1000 genomes]
rs559574	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56086412	0.80[AFR][1000 genomes]
rs56115002	0.80[AFR][1000 genomes]
rs56153113	0.80[AFR][1000 genomes]
rs56160758	0.80[AFR][1000 genomes]
rs56246849	0.81[AFR][1000 genomes]
rs6596659	0.82[AFR][1000 genomes]
rs6865618	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867271	0.82[AFR][1000 genomes]
rs6878136	0.94[ASN][1000 genomes]
rs6883467	0.80[AFR][1000 genomes]
rs6890358	0.80[AFR][1000 genomes]
rs6895358	0.80[AFR][1000 genomes]
rs709390	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7710032	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7711061	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7712408	0.89[ASN][1000 genomes]
rs7719375	0.81[AFR][1000 genomes]
rs7719562	1.00[ASN][1000 genomes]
rs7719649	1.00[ASN][1000 genomes]
rs7723242	0.94[ASN][1000 genomes]
rs819232	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9327955	0.80[AFR][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	nsv1024391	chr5:98355665-98653657	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv599118	chr5:98358191-99029453	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv599119	chr5:98358191-99315677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6885458	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98380400-98381800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:98380800-98383600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:98381000-98381800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:98381000-98381800	Enhancers	Fetal Lung	lung
5	chr5:98381200-98381800	Enhancers	Liver	Liver
6	chr5:98381200-98382400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr5:98381200-98382800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:98381400-98382200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:98381400-98382600	Enhancers	Primary T cells from cord blood	blood
10	chr5:98381400-98386800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:98381600-98381800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:98381600-98382400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:98381600-98395800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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