Variant report

Variant	rs161947
Chromosome Location	chr5:98268572-98268573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
2	chr5:98266485..98269344-chr6:26198000..26199535,2	MCF-7	breast:
3	chr5:98266316..98268754-chr5:98386981..98389928,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGMB-1	chr5:98264861-98270036	NONHSAT102968

Variant related genes	Relation type
ENSG00000197409	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000241597	Chromatin interaction

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

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

rs_ID	r²[population]
rs10479348	0.83[AMR][1000 genomes]
rs11242574	0.81[AMR][1000 genomes]
rs12515042	0.81[AMR][1000 genomes]
rs150935	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs152034	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1604450	0.81[AMR][1000 genomes]
rs161729	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs161730	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs161732	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs161744	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs161745	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs161746	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs161749	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs161750	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs161940	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs161957	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs167798	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2447826	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246251	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2545733	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2545737	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2545739	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2578576	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2578577	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs325195	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs326481	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs326482	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34488	0.84[AMR][1000 genomes]
rs34498	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs39660	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4343864	0.81[AMR][1000 genomes]
rs4583911	0.81[AMR][1000 genomes]
rs469519	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs709386	0.81[AMR][1000 genomes]
rs709387	0.81[AMR][1000 genomes]
rs709388	0.81[AMR][1000 genomes]
rs7449447	0.81[AMR][1000 genomes]
rs7719562	0.81[AMR][1000 genomes]
rs7719649	0.81[AMR][1000 genomes]
rs7723242	0.83[AMR][1000 genomes]
rs819227	0.81[AMR][1000 genomes]
rs819230	0.83[AMR][1000 genomes]
rs819231	0.83[AMR][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
rs161947	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266000-98269400	Weak transcription	Pancreas	Pancrea
2	chr5:98266000-98269800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:98266000-98271000	Weak transcription	Left Ventricle	heart
4	chr5:98266000-98272400	Weak transcription	Aorta	Aorta
5	chr5:98266000-98276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:98266000-98276400	Weak transcription	Placenta	Placenta
7	chr5:98266200-98268800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:98266200-98269000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr5:98266200-98269400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr5:98266200-98272600	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:98266200-98273200	Weak transcription	Right Ventricle	heart
12	chr5:98266200-98274200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
14	chr5:98266400-98269000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:98266400-98269200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:98266400-98270400	Weak transcription	HSMMtube	muscle
17	chr5:98266400-98270600	Weak transcription	NH-A	brain
18	chr5:98266400-98270600	Weak transcription	NHLF	lung
19	chr5:98266400-98270800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:98266400-98271000	Weak transcription	Psoas Muscle	Psoas
21	chr5:98266400-98271200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr5:98266400-98271400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr5:98266400-98271400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr5:98266400-98272400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr5:98266400-98272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:98266400-98273000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:98266400-98273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:98266400-98273400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:98266400-98276200	Weak transcription	Fetal Kidney	kidney
30	chr5:98266600-98268800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:98266600-98268800	Weak transcription	NHEK	skin
32	chr5:98266600-98269000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:98266600-98269200	Weak transcription	Right Atrium	heart
34	chr5:98266600-98270200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:98266600-98270200	Weak transcription	Osteobl	bone
36	chr5:98266600-98270400	Weak transcription	A549	lung
37	chr5:98266600-98270400	Weak transcription	HSMM	muscle
38	chr5:98266600-98270600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:98266600-98272000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr5:98266600-98273400	Weak transcription	NHDF-Ad	bronchial
41	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
42	chr5:98266800-98268600	Weak transcription	Liver	Liver
43	chr5:98266800-98268800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:98266800-98268800	Weak transcription	Thymus	Thymus
45	chr5:98266800-98269000	Weak transcription	Brain Angular Gyrus	brain
46	chr5:98266800-98269600	Weak transcription	Fetal Brain Male	brain
47	chr5:98266800-98270400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr5:98266800-98270600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:98266800-98273200	Weak transcription	HUVEC	blood vessel
50	chr5:98266800-98274000	Weak transcription	Fetal Lung	lung

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