Variant report

Variant	rs34496
Chromosome Location	chr5:98299516-98299517
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98263389..98266145-chr5:98295951..98300561,6	K562	blood:
2	chr5:98263064..98266794-chr5:98295400..98300838,7	K562	blood:
3	chr5:98298928..98301270-chr5:98305574..98308341,2	K562	blood:
4	chr5:98297682..98299622-chr5:98302405..98305273,3	K562	blood:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10037147	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10038192	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10040066	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10050423	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10076291	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10477857	0.93[ASN][1000 genomes]
rs10479344	0.84[EUR][1000 genomes]
rs10479345	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10479346	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10479348	0.81[ASN][1000 genomes]
rs1093794	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1104262	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11242567	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11949103	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950452	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950855	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11960896	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12109067	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12189335	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13179812	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1393210	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1472622	0.96[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs161729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs161730	0.98[ASN][1000 genomes]
rs161731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161732	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs161935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161941	0.84[CEU][hapmap]
rs162150	0.84[CEU][hapmap]
rs162337	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs162341	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167798	0.98[ASN][1000 genomes]
rs172874	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875529	1.00[CHB][hapmap]
rs2221268	1.00[CHB][hapmap]
rs2455423	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927647	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2927648	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927654	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937706	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937708	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937709	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs325195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs325220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326468	0.84[CEU][hapmap]
rs326480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs326481	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs326482	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs326493	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327807	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34488	0.98[ASN][1000 genomes]
rs34489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34490	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34491	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34497	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34498	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34499	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs363929	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs366000	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs366353	0.96[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs370529	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs377731	0.81[EUR][1000 genomes]
rs378089	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380156	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393697	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs395668	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs398436	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs407562	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs416750	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs422127	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs428836	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs434039	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443726	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4448016	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs447044	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs449204	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs451141	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4565239	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4583911	1.00[CHB][hapmap]
rs45931	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs467728	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs469018	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4703048	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4703049	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4703051	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4703052	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703340	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs539024	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs559574	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6865618	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6878136	1.00[CHB][hapmap]
rs6885458	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs709386	0.93[ASN][1000 genomes]
rs709387	0.93[ASN][1000 genomes]
rs709388	0.93[ASN][1000 genomes]
rs709389	0.93[ASN][1000 genomes]
rs709390	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7710032	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7711061	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7719562	1.00[CHB][hapmap]
rs819227	0.93[ASN][1000 genomes]
rs819230	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs819231	0.93[ASN][1000 genomes]
rs819232	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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	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
rs34496	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98297200-98299800	Enhancers	Thymus	Thymus
2	chr5:98297400-98300800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr5:98297800-98299600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr5:98297800-98299800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:98298200-98299600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr5:98298200-98299600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:98298200-98299800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:98298200-98299800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr5:98298200-98300200	Enhancers	Fetal Thymus	thymus
10	chr5:98298400-98299600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:98298400-98299600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr5:98298400-98301600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:98298600-98299600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:98298600-98299800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:98299000-98299600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:98299000-98299600	Enhancers	K562	blood
17	chr5:98299200-98299600	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr5:98299400-98300000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr5:98299400-98300600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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