Variant report

Variant	rs161744
Chromosome Location	chr5:98261891-98261892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:98260830-98273878	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98220809..98224769-chr5:98261722..98266325,5	K562	blood:
2	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248489	TF binding region
ENSG00000153922	Chromatin interaction
ENSG00000200351	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10050804	0.82[AMR][1000 genomes]
rs10479348	0.81[AMR][1000 genomes]
rs150935	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161729	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs161730	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs161734	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161736	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161737	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161738	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161739	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161749	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161750	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161940	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161945	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161947	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs161957	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167798	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2447826	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2545733	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545734	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2545735	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545736	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545737	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545738	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545739	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545740	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578576	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578577	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617514	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325195	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs325199	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325203	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325204	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325208	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs325209	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325214	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326487	0.91[EUR][1000 genomes];1.00[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];0.95[ASN][1000 genomes]
rs331928	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34488	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs469519	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723242	0.81[AMR][1000 genomes]
rs819230	0.81[AMR][1000 genomes]
rs819231	0.81[AMR][1000 genomes]
rs992774	0.86[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
rs161744	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 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	chr5:98228400-98263000	Weak transcription	Aorta	Aorta
4	chr5:98235000-98262600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:98235400-98262600	Weak transcription	Fetal Brain Male	brain
6	chr5:98236400-98263200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:98236600-98263000	Weak transcription	Ovary	ovary
8	chr5:98236800-98263000	Weak transcription	Brain Substantia Nigra	brain
9	chr5:98240200-98263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:98240800-98263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:98247400-98262600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:98247600-98262200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:98247600-98262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:98249800-98262000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:98253200-98263000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:98253800-98262600	Weak transcription	NHLF	lung
17	chr5:98254000-98262200	Strong transcription	Placenta	Placenta
18	chr5:98254200-98262000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:98254600-98262200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:98255200-98263000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:98255400-98262200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr5:98255600-98262000	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr5:98256800-98262000	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr5:98257200-98262600	Weak transcription	Brain Angular Gyrus	brain
25	chr5:98257200-98262600	Weak transcription	Psoas Muscle	Psoas
26	chr5:98257200-98262800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:98257800-98262400	Weak transcription	Right Atrium	heart
28	chr5:98258000-98262200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:98258600-98262200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr5:98258600-98262800	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:98258800-98262200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:98258800-98262200	Genic enhancers	Monocytes-CD14+_RO01746	blood
33	chr5:98258800-98262600	Weak transcription	Stomach Mucosa	stomach
34	chr5:98259400-98262400	Weak transcription	Brain Germinal Matrix	brain
35	chr5:98259600-98262200	Enhancers	Primary T cells from cord blood	blood
36	chr5:98259800-98262000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr5:98259800-98262000	Weak transcription	NHEK	skin
38	chr5:98259800-98262600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:98260000-98262200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:98260000-98262400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:98260000-98262400	Weak transcription	Right Ventricle	heart
42	chr5:98260000-98262400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:98260000-98262600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:98260000-98263000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:98260000-98263000	Weak transcription	Gastric	stomach
46	chr5:98260000-98263000	Weak transcription	Pancreas	Pancrea
47	chr5:98260000-98263600	Weak transcription	Spleen	Spleen
48	chr5:98260400-98262400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:98260400-98262400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr5:98260400-98262800	Weak transcription	H9 Cell Line	embryonic stem cell

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