Variant report

Variant	rs34499
Chromosome Location	chr5:98295538-98295539
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98250278..98252358-chr5:98294298..98296152,2	K562	blood:
2	chr5:98289511..98291759-chr5:98293576..98296217,2	K562	blood:
3	chr5:98263064..98266794-chr5:98295400..98300838,7	K562	blood:
4	chr5:98262886..98265417-chr5:98293369..98295654,3	K562	blood:
5	chr5:98290036..98292001-chr5:98294235..98296369,4	K562	blood:

Variant related genes	Relation type
ENSG00000241597	Chromatin interaction
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10037147	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10038192	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10040066	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10050423	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10076291	0.91[EUR][1000 genomes]
rs10479344	0.82[EUR][1000 genomes]
rs10479345	0.91[EUR][1000 genomes]
rs10479346	0.91[EUR][1000 genomes]
rs1093794	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1104262	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11242567	0.86[EUR][1000 genomes]
rs11949103	0.91[EUR][1000 genomes]
rs11950452	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11950855	0.91[EUR][1000 genomes]
rs11960896	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12109067	0.87[EUR][1000 genomes]
rs12189335	0.90[EUR][1000 genomes]
rs13179812	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1393210	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1472622	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs151102	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161731	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs161732	0.84[ASN][1000 genomes]
rs161935	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs161936	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs162337	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162341	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs172874	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2455423	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs246251	0.94[ASN][1000 genomes]
rs2927647	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2927648	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2927654	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2937706	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2937708	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2937709	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs325220	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs326480	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326481	1.00[ASN][1000 genomes]
rs326482	1.00[ASN][1000 genomes]
rs326493	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs327807	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34489	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34490	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34491	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34496	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34497	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34498	1.00[ASN][1000 genomes]
rs363929	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs366000	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs366353	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs370529	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs377731	0.81[EUR][1000 genomes]
rs378089	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs380156	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs393697	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs395668	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs39660	0.96[ASN][1000 genomes]
rs398436	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs40075	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs407562	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs416750	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs422127	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs428836	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434039	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs443726	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4448016	0.85[EUR][1000 genomes]
rs447044	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs449204	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs451141	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4565239	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs45931	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs467728	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469018	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703048	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4703049	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4703051	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4703052	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4703340	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs539024	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs559574	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6865618	0.85[EUR][1000 genomes]
rs6885458	0.85[EUR][1000 genomes]
rs709390	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7710032	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7711061	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs819232	0.89[AMR][1000 genomes];0.93[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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34499	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
2	chr5:98278600-98299400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:98279400-98298400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:98290600-98296800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:98294800-98297200	Enhancers	K562	blood
6	chr5:98295000-98296000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:98295000-98296800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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