Variant report

Variant	rs161948
Chromosome Location	chr5:98268037-98268038
allele	A/G
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	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:
3	chr5:98265027..98268409-chr5:98365166..98367986,4	K562	blood:
4	chr5:98266485..98269344-chr6:26198000..26199535,2	MCF-7	breast:
5	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
ENSG00000241597	Chromatin interaction
ENSG00000200351	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000197409	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1472622	0.81[AMR][1000 genomes]
rs150991	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs150992	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs151102	0.86[EUR][1000 genomes]
rs161731	0.81[EUR][1000 genomes]
rs161735	0.90[ASN][1000 genomes]
rs161740	0.90[ASN][1000 genomes]
rs161747	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs161933	0.90[ASN][1000 genomes]
rs161938	0.90[ASN][1000 genomes]
rs161939	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs161941	0.90[ASN][1000 genomes]
rs161942	0.90[ASN][1000 genomes]
rs161950	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs161951	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs161952	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161953	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs161954	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs161956	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs162140	0.90[ASN][1000 genomes]
rs162149	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs162150	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs172874	0.81[EUR][1000 genomes]
rs2617507	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2937706	0.81[EUR][1000 genomes]
rs2937708	0.81[EUR][1000 genomes]
rs325200	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs325217	0.90[ASN][1000 genomes]
rs325220	0.81[EUR][1000 genomes]
rs326463	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs326464	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs326468	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs326469	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs326480	0.86[EUR][1000 genomes]
rs326485	0.90[ASN][1000 genomes]
rs326489	0.90[ASN][1000 genomes]
rs327792	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs327793	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs327803	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs327807	0.81[EUR][1000 genomes]
rs327811	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs330419	0.90[ASN][1000 genomes]
rs330421	0.90[ASN][1000 genomes]
rs330422	0.90[ASN][1000 genomes]
rs331926	0.86[ASN][1000 genomes]
rs331929	0.90[ASN][1000 genomes]
rs331931	0.90[ASN][1000 genomes]
rs34495	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs366353	0.81[AMR][1000 genomes]
rs428836	0.84[EUR][1000 genomes]
rs447044	0.81[AMR][1000 genomes]
rs45931	0.81[EUR][1000 genomes]
rs466340	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs467728	0.84[EUR][1000 genomes]
rs4703049	0.81[AMR][1000 genomes]
rs692832	0.90[ASN][1000 genomes]
rs751878	0.83[ASN][1000 genomes]
rs7710032	0.81[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
rs161948	RGMB	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266000-98268200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:98266000-98269400	Weak transcription	Pancreas	Pancrea
3	chr5:98266000-98269800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:98266000-98271000	Weak transcription	Left Ventricle	heart
5	chr5:98266000-98272400	Weak transcription	Aorta	Aorta
6	chr5:98266000-98276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:98266000-98276400	Weak transcription	Placenta	Placenta
8	chr5:98266200-98268800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:98266200-98269000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr5:98266200-98269400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:98266200-98272600	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:98266200-98273200	Weak transcription	Right Ventricle	heart
13	chr5:98266200-98274200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
15	chr5:98266400-98269000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr5:98266400-98269200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:98266400-98270400	Weak transcription	HSMMtube	muscle
18	chr5:98266400-98270600	Weak transcription	NH-A	brain
19	chr5:98266400-98270600	Weak transcription	NHLF	lung
20	chr5:98266400-98270800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:98266400-98271000	Weak transcription	Psoas Muscle	Psoas
22	chr5:98266400-98271200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr5:98266400-98271400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr5:98266400-98271400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr5:98266400-98272400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:98266400-98272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:98266400-98273000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:98266400-98273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:98266400-98273400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:98266400-98276200	Weak transcription	Fetal Kidney	kidney
31	chr5:98266600-98268800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:98266600-98268800	Weak transcription	NHEK	skin
33	chr5:98266600-98269000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:98266600-98269200	Weak transcription	Right Atrium	heart
35	chr5:98266600-98270200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:98266600-98270200	Weak transcription	Osteobl	bone
37	chr5:98266600-98270400	Weak transcription	A549	lung
38	chr5:98266600-98270400	Weak transcription	HSMM	muscle
39	chr5:98266600-98270600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:98266600-98272000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr5:98266600-98273400	Weak transcription	NHDF-Ad	bronchial
42	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
43	chr5:98266800-98268600	Weak transcription	Liver	Liver
44	chr5:98266800-98268800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:98266800-98268800	Weak transcription	Thymus	Thymus
46	chr5:98266800-98269000	Weak transcription	Brain Angular Gyrus	brain
47	chr5:98266800-98269600	Weak transcription	Fetal Brain Male	brain
48	chr5:98266800-98270400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr5:98266800-98270600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr5:98266800-98273200	Weak transcription	HUVEC	blood vessel

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