Variant report

Variant	rs161745
Chromosome Location	chr5:98260721-98260722
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98258735..98261522-chr5:98261609..98263203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153922	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]
rs161744	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
rs161745	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	chr5:98235200-98261600	Weak transcription	Fetal Kidney	kidney
6	chr5:98235400-98262600	Weak transcription	Fetal Brain Male	brain
7	chr5:98236400-98263200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:98236600-98261000	Weak transcription	Small Intestine	intestine
9	chr5:98236600-98261600	Weak transcription	Fetal Brain Female	brain
10	chr5:98236600-98263000	Weak transcription	Ovary	ovary
11	chr5:98236800-98263000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:98240200-98263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:98240800-98263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:98247400-98262600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:98247600-98262200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:98247600-98262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:98248000-98261600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:98249000-98261400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:98249800-98262000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:98251400-98261000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:98252600-98261200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:98253000-98261800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr5:98253200-98261200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:98253200-98263000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:98253400-98261000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:98253600-98261200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr5:98253600-98261600	Strong transcription	Fetal Intestine Large	intestine
28	chr5:98253600-98261800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:98253800-98260800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:98253800-98262600	Weak transcription	NHLF	lung
31	chr5:98254000-98261000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:98254000-98261200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:98254000-98262200	Strong transcription	Placenta	Placenta
34	chr5:98254200-98262000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:98254600-98261200	Strong transcription	Liver	Liver
36	chr5:98254600-98261400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:98254600-98261600	Strong transcription	HMEC	breast
38	chr5:98254600-98261600	Strong transcription	NH-A	brain
39	chr5:98254600-98261800	Strong transcription	Osteobl	bone
40	chr5:98254600-98262200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:98254800-98261000	Strong transcription	HSMM	muscle
42	chr5:98254800-98261800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:98255000-98261600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr5:98255200-98261600	Strong transcription	Fetal Muscle Leg	muscle
45	chr5:98255200-98261800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:98255200-98263000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr5:98255400-98261600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:98255400-98261600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr5:98255400-98261600	Strong transcription	Fetal Lung	lung
50	chr5:98255400-98261800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links