Variant report

Variant	rs161943
Chromosome Location	chr5:98282677-98282678
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10050804	0.80[AMR][1000 genomes]
rs10479348	0.83[AMR][1000 genomes]
rs11242574	0.81[AMR][1000 genomes]
rs12515042	0.81[AMR][1000 genomes]
rs1604450	0.81[AMR][1000 genomes]
rs161729	0.85[AMR][1000 genomes]
rs161730	0.85[AMR][1000 genomes]
rs161732	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs167798	0.85[AMR][1000 genomes]
rs246251	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs325195	0.85[AMR][1000 genomes]
rs326481	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs326482	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34488	0.85[AMR][1000 genomes]
rs39660	0.80[AMR][1000 genomes]
rs4343864	0.81[AMR][1000 genomes]
rs4583911	0.81[AMR][1000 genomes]
rs4703345	0.80[AMR][1000 genomes]
rs6878136	0.80[AMR][1000 genomes]
rs709386	0.82[AMR][1000 genomes]
rs709387	0.82[AMR][1000 genomes]
rs709388	0.82[AMR][1000 genomes]
rs7449447	0.82[AMR][1000 genomes]
rs7719562	0.81[AMR][1000 genomes]
rs7719649	0.81[AMR][1000 genomes]
rs7723242	0.83[AMR][1000 genomes]
rs819227	0.82[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	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
4	esv3433359	chr5:98282481-98282767	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs161943	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 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	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:98274800-98282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
6	chr5:98276600-98282800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:98277200-98283000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:98277600-98283000	Weak transcription	HMEC	breast
9	chr5:98278600-98299400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:98279400-98298400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:98280600-98283000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr5:98281400-98283400	Enhancers	Right Atrium	heart
13	chr5:98281600-98283600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:98281800-98283000	Weak transcription	Left Ventricle	heart
15	chr5:98282200-98283000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:98282200-98283200	Weak transcription	Right Ventricle	heart
17	chr5:98282400-98282800	Weak transcription	Brain Substantia Nigra	brain
18	chr5:98282400-98283800	Enhancers	K562	blood
19	chr5:98282600-98290400	Weak transcription	Brain Hippocampus Middle	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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