Variant report

Variant	rs2545738
Chromosome Location	chr5:98175225-98175226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs150935	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152034	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161734	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161736	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161737	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161738	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161739	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161744	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161745	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161746	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161749	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161750	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161940	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161945	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161957	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545733	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545734	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2545735	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545736	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545737	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545739	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545740	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578576	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578577	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617514	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325199	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325203	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325204	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325208	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs325209	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325214	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326487	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331541	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs331542	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs331544	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs331548	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331927	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331928	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469519	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992774	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[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	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2545738	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98161000-98175400	Weak transcription	Primary T cells from cord blood	blood
2	chr5:98170400-98176600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:98172200-98179800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:98175000-98175400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr5:98175000-98175400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr5:98175000-98175600	Active TSS	Fetal Intestine Large	intestine
7	chr5:98175000-98175600	Active TSS	Fetal Stomach	stomach
8	chr5:98175000-98175600	Active TSS	HUVEC	blood vessel
9	chr5:98175000-98175800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr5:98175000-98175800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:98175000-98175800	Active TSS	Primary hematopoietic stem cells	blood
12	chr5:98175000-98175800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:98175000-98175800	Active TSS	Adipose Nuclei	Adipose
14	chr5:98175000-98175800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr5:98175000-98175800	Active TSS	Fetal Kidney	kidney
16	chr5:98175000-98175800	Active TSS	Fetal Muscle Leg	muscle
17	chr5:98175000-98175800	Active TSS	Stomach Smooth Muscle	stomach
18	chr5:98175000-98175800	Active TSS	Thymus	Thymus
19	chr5:98175000-98175800	Active TSS	Osteobl	bone
20	chr5:98175000-98176000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:98175000-98176000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:98175000-98176000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr5:98175200-98175400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:98175200-98175400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:98175200-98175400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:98175200-98175400	Active TSS	Left Ventricle	heart
27	chr5:98175200-98175400	Enhancers	Spleen	Spleen
28	chr5:98175200-98175600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:98175200-98175600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr5:98175200-98175600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:98175200-98175600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:98175200-98175600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:98175200-98175600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:98175200-98175600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:98175200-98175600	Flanking Active TSS	Liver	Liver
36	chr5:98175200-98175600	Active TSS	Fetal Brain Female	brain
37	chr5:98175200-98175600	Active TSS	Placenta Amnion	Placenta Amnion
38	chr5:98175200-98175600	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr5:98175200-98175800	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr5:98175200-98175800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:98175200-98175800	Active TSS	Duodenum Mucosa	Duodenum
42	chr5:98175200-98175800	Active TSS	Fetal Intestine Small	intestine
43	chr5:98175200-98175800	Active TSS	Ovary	ovary
44	chr5:98175200-98175800	Active TSS	Right Atrium	heart
45	chr5:98175200-98175800	Active TSS	Right Ventricle	heart
46	chr5:98175200-98175800	Active TSS	NHLF	lung
47	chr5:98175200-98176000	Active TSS	Duodenum Smooth Muscle	Duodenum

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