Variant report

Variant	rs246251
Chromosome Location	chr5:98278066-98278067
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98272097..98275128-chr5:98275593..98280478,6	MCF-7	breast:
2	chr5:98276533..98278644-chr5:98288923..98290589,2	K562	blood:
3	chr5:98263406..98266421-chr5:98277549..98281338,5	MCF-7	breast:
4	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241597	Chromatin interaction
ENSG00000248489	Chromatin interaction
ENSG00000153922	Chromatin interaction
ENSG00000200351	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10050804	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10479348	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11242574	0.85[AMR][1000 genomes]
rs11745405	0.84[AMR][1000 genomes]
rs12515042	0.85[AMR][1000 genomes]
rs151102	0.94[ASN][1000 genomes]
rs1604450	0.85[AMR][1000 genomes]
rs161729	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs161730	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs161732	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs161943	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs161947	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs162337	0.94[ASN][1000 genomes]
rs167798	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1875529	0.80[AMR][1000 genomes]
rs2447826	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs325195	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs326480	0.94[ASN][1000 genomes]
rs326481	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs326482	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs327807	1.00[ASN][1000 genomes]
rs34488	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34498	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34499	0.94[ASN][1000 genomes]
rs39660	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs428836	0.94[ASN][1000 genomes]
rs4343864	0.85[AMR][1000 genomes]
rs4583911	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs467728	0.94[ASN][1000 genomes]
rs469018	0.94[ASN][1000 genomes]
rs4703345	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6878136	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs709386	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs709387	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs709388	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs709389	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7449447	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7719562	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7719649	0.85[AMR][1000 genomes]
rs7723242	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs819227	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs819230	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs819231	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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
rs246251	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
2	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
3	chr5:98266800-98278400	Weak transcription	Hela-S3	cervix
4	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:98272600-98278600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr5:98274600-98280000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr5:98274800-98278800	Weak transcription	HepG2	liver
8	chr5:98274800-98282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
10	chr5:98276000-98278600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr5:98276200-98278200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:98276200-98278800	Enhancers	Primary B cells from cord blood	blood
13	chr5:98276200-98281600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:98276400-98278200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr5:98276600-98282800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:98277000-98278800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:98277000-98279200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:98277200-98278400	Weak transcription	Fetal Lung	lung
19	chr5:98277200-98280000	Weak transcription	Psoas Muscle	Psoas
20	chr5:98277200-98281200	Weak transcription	Right Ventricle	heart
21	chr5:98277200-98282000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:98277200-98283000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:98277400-98278800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:98277400-98279000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:98277400-98281600	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:98277400-98282000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:98277400-98282000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:98277400-98282200	Weak transcription	Brain Substantia Nigra	brain
29	chr5:98277600-98278600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:98277600-98281400	Weak transcription	Left Ventricle	heart
31	chr5:98277600-98281800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:98277600-98283000	Weak transcription	HMEC	breast
33	chr5:98277800-98278800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:98277800-98279000	Weak transcription	Placenta	Placenta
35	chr5:98277800-98279400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr5:98277800-98280200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:98277800-98281000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:98277800-98281400	Weak transcription	Right Atrium	heart
39	chr5:98278000-98278400	Weak transcription	Fetal Muscle Leg	muscle
40	chr5:98278000-98278400	Weak transcription	K562	blood
41	chr5:98278000-98279200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr5:98278000-98279800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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