Variant report

Variant	rs218060
Chromosome Location	chr2:86841879-86841880
allele	G/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	chr2:86841830-86842411	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86839004..86842325-chr2:86847581..86852030,6	MCF-7	breast:
2	chr2:86788830..86791431-chr2:86840608..86843450,2	MCF-7	breast:

Variant related genes	Relation type
RNF103	TF binding region
ENSG00000228363	Chromatin interaction
ENSG00000249884	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000115561	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10185085	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs1036940	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs11127040	1.00[CHB][hapmap]
rs11127042	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs11127047	0.85[GIH][hapmap]
rs11693352	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs12714185	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs12714187	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs12995117	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs1468039	1.00[CHB][hapmap]
rs1518811	1.00[CHB][hapmap]
rs2030259	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2044230	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2120340	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs308901	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs308902	0.81[MEX][hapmap]
rs308903	0.81[MEX][hapmap]
rs308907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs308911	0.91[CEU][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs396354	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs433655	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap]
rs4832285	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs4832289	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs4832294	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs4832298	0.89[ASN][1000 genomes]
rs6547700	1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap]
rs6714826	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs6714957	0.96[ASN][1000 genomes]
rs683139	0.85[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7557796	0.85[GIH][hapmap]
rs7574389	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs950780	1.00[CHB][hapmap]
rs966477	1.00[CHB][hapmap];0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs218060	IMMT	cis	lymphoblastoid	seeQTL
rs218060	GGCX	cis	cerebellum	SCAN
rs218060	VPS24	cis	lymphoblastoid	seeQTL
rs218060	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs218060	PTCD3	cis	cerebellum	SCAN
rs218060	POLR1A	cis	cerebellum	SCAN
rs218060	RNF103	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86823200-86842800	Weak transcription	Psoas Muscle	Psoas
2	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:86826800-86842000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:86826800-86847800	Weak transcription	NHEK	skin
5	chr2:86828200-86847800	Weak transcription	NHLF	lung
6	chr2:86829000-86845400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:86829400-86848400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:86829400-86849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:86829600-86846200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:86829800-86846000	Weak transcription	NH-A	brain
11	chr2:86829800-86849400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:86830000-86846200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:86830000-86848600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:86830400-86846200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:86830400-86847600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:86830400-86848600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:86830600-86847000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:86830800-86845000	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:86830800-86845600	Strong transcription	Dnd41	blood
20	chr2:86830800-86847600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:86830800-86847800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:86830800-86848000	Strong transcription	Placenta	Placenta
23	chr2:86831000-86842600	Strong transcription	Liver	Liver
24	chr2:86831000-86842800	Strong transcription	Fetal Intestine Large	intestine
25	chr2:86831000-86847200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:86831800-86843200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:86831800-86848000	Weak transcription	HMEC	breast
28	chr2:86831800-86848200	Weak transcription	K562	blood
29	chr2:86832200-86848200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:86832400-86849400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:86832600-86844600	Weak transcription	Fetal Brain Male	brain
32	chr2:86832600-86844600	Weak transcription	Small Intestine	intestine
33	chr2:86832600-86848200	Weak transcription	Colonic Mucosa	Colon
34	chr2:86833000-86848200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:86834000-86846800	Strong transcription	Fetal Lung	lung
36	chr2:86834400-86842800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:86834400-86846600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr2:86834400-86847000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:86834600-86844600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr2:86834600-86847400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:86834600-86847800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:86835200-86843000	Strong transcription	A549	lung
43	chr2:86835200-86843200	Strong transcription	Brain Anterior Caudate	brain
44	chr2:86835200-86847200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr2:86835200-86847800	Weak transcription	Hela-S3	cervix
46	chr2:86835400-86845200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:86835400-86846600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:86835600-86842600	Strong transcription	Brain Germinal Matrix	brain
49	chr2:86835600-86843600	Strong transcription	Primary B cells from cord blood	blood
50	chr2:86835600-86844000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links