Variant report

Variant	rs1867819
Chromosome Location	chr2:46962739-46962740
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46961327..46962989-chr2:46966754..46968655,2	K562	blood:
2	chr2:46925232..46928034-chr2:46961115..46963290,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1009230	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1009231	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10167561	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10168342	0.95[CHB][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs11125087	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12475080	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1456009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1471056	0.91[ASN][1000 genomes]
rs1471057	0.82[ASN][1000 genomes]
rs1813505	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045291	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2061182	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3768720	0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs3814039	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4361172	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4522653	0.95[CHB][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs4953415	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953418	0.84[ASN][1000 genomes]
rs6544917	0.81[ASN][1000 genomes]
rs6544918	0.90[ASN][1000 genomes]
rs6544919	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544921	0.83[ASN][1000 genomes]
rs6705847	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6718677	0.86[ASN][1000 genomes]
rs6721122	0.85[ASN][1000 genomes]
rs6726345	0.87[ASN][1000 genomes]
rs6727737	0.82[ASN][1000 genomes]
rs6727934	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6728559	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6728881	0.86[EUR][1000 genomes]
rs6730949	0.87[ASN][1000 genomes]
rs6741706	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6746471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6748938	0.95[CHB][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs7570376	0.91[ASN][1000 genomes]
rs7580649	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs897528	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.94[ASN][1000 genomes]
rs958726	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs970711	0.94[MEX][hapmap]
rs991742	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1013079	chr2:46949337-46998417	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1867819	SOCS5	cis	multi-tissue	Pritchard
rs1867819	PIGF	cis	multi-tissue	Pritchard

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46945400-46985400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:46947600-46975600	Weak transcription	HSMM	muscle
3	chr2:46948200-46964400	Weak transcription	NHEK	skin
4	chr2:46948200-46967400	Weak transcription	Esophagus	oesophagus
5	chr2:46948200-46974600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:46948200-46977200	Weak transcription	Aorta	Aorta
7	chr2:46948600-46964200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:46948600-46964400	Weak transcription	NH-A	brain
9	chr2:46948600-46974400	Weak transcription	Fetal Stomach	stomach
10	chr2:46950800-46975400	Weak transcription	Fetal Lung	lung
11	chr2:46953400-46964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:46955000-46975400	Weak transcription	Small Intestine	intestine
13	chr2:46955200-46964600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:46955200-46967600	Weak transcription	Thymus	Thymus
15	chr2:46955200-46970400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:46955200-46974400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:46955200-46984800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr2:46955200-46985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:46955400-46967600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:46955400-46967800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:46955400-46967800	Weak transcription	Fetal Thymus	thymus
22	chr2:46955400-46974200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:46956000-46964200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:46956000-46975400	Weak transcription	Lung	lung
25	chr2:46956000-46980000	Weak transcription	Right Atrium	heart
26	chr2:46956200-46963600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:46957400-46973200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:46958000-46964600	Weak transcription	HMEC	breast
29	chr2:46958800-46964200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:46959600-46967000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:46959600-46967200	Weak transcription	Ovary	ovary
32	chr2:46959600-46975000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:46959800-46969000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:46960000-46963800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:46960000-46964200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:46960000-46964400	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:46960000-46978800	Weak transcription	Primary T cells from cord blood	blood
38	chr2:46960000-46988000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:46960600-46962800	Genic enhancers	Osteobl	bone
40	chr2:46960600-46963200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:46960800-46965800	Enhancers	HepG2	liver
42	chr2:46961000-46964200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:46961800-46962800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:46961800-46962800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:46961800-46962800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:46961800-46962800	Genic enhancers	A549	lung
47	chr2:46961800-46963400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:46961800-46965000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:46962000-46962800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr2:46962000-46962800	Enhancers	Duodenum Smooth Muscle	Duodenum

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