Variant report

Variant	rs2545737
Chromosome Location	chr5:98247222-98247223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98244197..98249513-chr5:98262735..98266592,9	MCF-7	breast:
2	chr5:98244721..98249104-chr5:98263140..98266489,8	K562	blood:
3	chr5:98245669..98247917-chr5:98393719..98395372,2	K562	blood:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs150935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152034	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs161729	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs161730	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs161734	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161736	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161737	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161738	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161739	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161744	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161745	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161746	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs161749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs161750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs161945	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161947	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs161957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs167798	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2447826	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2545733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545734	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2545735	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545736	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545738	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545740	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2578576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2578577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2617514	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs325195	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs325199	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs325203	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs325204	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs325208	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs325209	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs325214	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs326487	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs331541	0.86[EUR][1000 genomes]
rs331542	0.84[EUR][1000 genomes]
rs331544	0.86[EUR][1000 genomes]
rs331548	0.85[EUR][1000 genomes]
rs331927	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs331928	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34488	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs469519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs992774	0.86[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	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	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
rs2545737	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98200000-98263000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:98215000-98263000	Weak transcription	Esophagus	oesophagus
3	chr5:98225800-98258400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:98228200-98259200	Weak transcription	Spleen	Spleen
5	chr5:98228400-98259200	Weak transcription	Gastric	stomach
6	chr5:98228400-98259400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:98228400-98263000	Weak transcription	Aorta	Aorta
8	chr5:98232000-98254200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:98232000-98258200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:98232000-98259200	Weak transcription	Pancreas	Pancrea
11	chr5:98235000-98262600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:98235200-98261600	Weak transcription	Fetal Kidney	kidney
13	chr5:98235400-98262600	Weak transcription	Fetal Brain Male	brain
14	chr5:98236000-98256800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:98236400-98256600	Weak transcription	Lung	lung
16	chr5:98236400-98258400	Weak transcription	Brain Germinal Matrix	brain
17	chr5:98236400-98263200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:98236600-98248000	Weak transcription	Fetal Intestine Small	intestine
19	chr5:98236600-98248000	Weak transcription	Fetal Stomach	stomach
20	chr5:98236600-98249600	Weak transcription	Psoas Muscle	Psoas
21	chr5:98236600-98257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:98236600-98259000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:98236600-98261000	Weak transcription	Small Intestine	intestine
24	chr5:98236600-98261600	Weak transcription	Fetal Brain Female	brain
25	chr5:98236600-98263000	Weak transcription	Ovary	ovary
26	chr5:98236800-98248000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr5:98236800-98249800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:98236800-98253600	Weak transcription	Left Ventricle	heart
29	chr5:98236800-98254000	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:98236800-98256000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:98236800-98263000	Weak transcription	Brain Substantia Nigra	brain
32	chr5:98237000-98248000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:98237000-98252800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:98237000-98256000	Weak transcription	HSMMtube	muscle
35	chr5:98237000-98258600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr5:98237000-98259200	Weak transcription	Colonic Mucosa	Colon
37	chr5:98239200-98252800	Weak transcription	NHLF	lung
38	chr5:98240000-98248000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:98240000-98248000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:98240200-98249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:98240200-98263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr5:98240400-98247400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:98240400-98249800	Weak transcription	Adipose Nuclei	Adipose
44	chr5:98240400-98249800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:98240600-98254600	Weak transcription	HMEC	breast
46	chr5:98240800-98247800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr5:98240800-98248200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:98240800-98248600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:98240800-98248600	Weak transcription	Placenta	Placenta
50	chr5:98240800-98249000	Weak transcription	HepG2	liver

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