Variant report

Variant	rs161954
Chromosome Location	chr5:98256537-98256538
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98254296..98256757-chr5:98393861..98395478,2	K562	blood:
2	chr5:98255571..98257201-chr5:98257380..98259074,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs150991	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs150992	0.81[AMR][1000 genomes]
rs161735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161933	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161936	0.84[CEU][hapmap]
rs161938	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161939	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161942	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161948	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs161950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161951	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs161952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs161953	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161956	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs162140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162473	0.86[EUR][1000 genomes]
rs162611	0.86[EUR][1000 genomes]
rs170734	0.80[EUR][1000 genomes]
rs193072	0.87[EUR][1000 genomes]
rs2545735	0.86[JPT][hapmap]
rs2617507	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs325200	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325217	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326463	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326464	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326469	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326485	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326489	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs327792	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327793	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs327803	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327811	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs330419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331543	0.87[EUR][1000 genomes]
rs331545	0.81[EUR][1000 genomes]
rs331549	0.80[EUR][1000 genomes]
rs331926	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs331929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331930	0.88[EUR][1000 genomes]
rs331931	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34489	0.84[CEU][hapmap]
rs34495	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs366353	0.81[CEU][hapmap]
rs466340	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860504	0.85[YRI][hapmap]
rs692832	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751878	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs992775	0.80[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
rs161954	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr5:98225800-98258400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:98228200-98259200	Weak transcription	Spleen	Spleen
5	chr5:98228400-98259200	Weak transcription	Gastric	stomach
6	chr5:98228400-98259400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:98228400-98263000	Weak transcription	Aorta	Aorta
8	chr5:98232000-98258200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:98232000-98259200	Weak transcription	Pancreas	Pancrea
10	chr5:98235000-98262600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:98235200-98261600	Weak transcription	Fetal Kidney	kidney
12	chr5:98235400-98262600	Weak transcription	Fetal Brain Male	brain
13	chr5:98236000-98256800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:98236400-98256600	Weak transcription	Lung	lung
15	chr5:98236400-98258400	Weak transcription	Brain Germinal Matrix	brain
16	chr5:98236400-98263200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:98236600-98257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:98236600-98259000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:98236600-98261000	Weak transcription	Small Intestine	intestine
20	chr5:98236600-98261600	Weak transcription	Fetal Brain Female	brain
21	chr5:98236600-98263000	Weak transcription	Ovary	ovary
22	chr5:98236800-98263000	Weak transcription	Brain Substantia Nigra	brain
23	chr5:98237000-98258600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:98237000-98259200	Weak transcription	Colonic Mucosa	Colon
25	chr5:98240200-98263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr5:98240800-98263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:98244400-98258400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:98247400-98256800	Weak transcription	Fetal Heart	heart
29	chr5:98247400-98256800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:98247400-98258400	Weak transcription	Right Ventricle	heart
31	chr5:98247400-98258800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:98247400-98259600	Weak transcription	Brain Anterior Caudate	brain
33	chr5:98247400-98262600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:98247600-98256800	Weak transcription	Brain Angular Gyrus	brain
35	chr5:98247600-98262200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:98247600-98262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr5:98248000-98261600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:98249000-98258400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:98249000-98261400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:98249800-98262000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:98250000-98256800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr5:98250000-98256800	Weak transcription	Right Atrium	heart
43	chr5:98250600-98256600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:98250800-98258400	Weak transcription	Colon Smooth Muscle	Colon
45	chr5:98251200-98257800	Weak transcription	Brain Hippocampus Middle	brain
46	chr5:98251400-98261000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:98252000-98257600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:98252600-98261200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:98252800-98256800	Weak transcription	NHEK	skin
50	chr5:98253000-98260200	Strong transcription	K562	blood

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