Variant report

Variant	rs161740
Chromosome Location	chr5:98205030-98205031
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	chr5:98204205..98207501-chr5:98263457..98266267,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1069182	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs150991	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs150992	1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs151102	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs161731	0.83[CEU][hapmap]
rs161735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161747	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161933	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161939	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161942	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161948	0.90[ASN][1000 genomes]
rs161950	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161951	0.95[EUR][1000 genomes]
rs161952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs161953	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161956	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162150	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162473	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs162611	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs170734	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs193072	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2545735	0.86[JPT][hapmap]
rs2617507	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs325200	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs325217	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325220	0.83[CEU][hapmap]
rs326463	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326464	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326468	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326469	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326480	0.82[CEU][hapmap]
rs326485	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326489	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327792	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs327793	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs327803	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs327811	0.95[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs330419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331543	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331545	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331549	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331918	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331926	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs331929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331930	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs331931	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34495	0.93[ASN][1000 genomes]
rs40075	0.83[CEU][hapmap]
rs466340	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs467728	0.82[CEU][hapmap]
rs692832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751878	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs992773	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs992775	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs161740	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	chr5:98180200-98213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:98186200-98213400	Weak transcription	Esophagus	oesophagus
3	chr5:98188400-98247000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:98189400-98205800	Weak transcription	Fetal Heart	heart
5	chr5:98189400-98227400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:98189600-98213800	Weak transcription	HSMMtube	muscle
7	chr5:98189600-98215400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:98189600-98241000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:98189800-98241000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr5:98189800-98241400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:98189800-98241400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:98189800-98241800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:98190000-98240600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:98190000-98240800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr5:98190000-98240800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:98190200-98240600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:98190200-98240600	Strong transcription	Liver	Liver
18	chr5:98190200-98241000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:98190400-98205400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:98190400-98212400	Weak transcription	Small Intestine	intestine
21	chr5:98190400-98213200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:98190400-98214600	Weak transcription	Aorta	Aorta
23	chr5:98190400-98224200	Strong transcription	Placenta	Placenta
24	chr5:98190400-98234600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:98190400-98238200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:98190400-98238800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:98190400-98240000	Weak transcription	Stomach Mucosa	stomach
28	chr5:98190400-98240400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:98190400-98240600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr5:98190400-98240800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr5:98190400-98241200	Strong transcription	Fetal Thymus	thymus
32	chr5:98190400-98243800	Strong transcription	Dnd41	blood
33	chr5:98190600-98209400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:98190600-98240600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:98190600-98240800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr5:98190600-98240800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:98190600-98241000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:98190800-98209800	Strong transcription	Adipose Nuclei	Adipose
39	chr5:98190800-98216200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:98190800-98226000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:98190800-98240000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr5:98191000-98225600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:98191000-98240800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr5:98191400-98213600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:98192200-98214600	Weak transcription	Brain Angular Gyrus	brain
46	chr5:98192400-98206000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:98193600-98219000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:98193800-98210000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:98194800-98206600	Strong transcription	Fetal Lung	lung
50	chr5:98195200-98240800	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links