Variant report

Variant	rs308902
Chromosome Location	chr2:86843758-86843759
allele	C/G
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	FOXA1	chr2:86843522-86844010	HepG2	liver:	n/a	n/a
2	CEBPB	chr2:86843748-86843951	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:86843485-86843979	HepG2	liver:	n/a	n/a
4	ARID3A	chr2:86843711-86843918	HepG2	liver:	n/a	n/a
5	SMC3	chr2:86843742-86843947	HepG2	liver:	n/a	n/a
6	CEBPB	chr2:86843740-86843940	A549	lung:	n/a	n/a
7	FOXA2	chr2:86843608-86843952	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86843538..86846012-chr2:86868633..86870186,2	MCF-7	breast:

Variant related genes	Relation type
RNF103	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1015117	0.91[GIH][hapmap]
rs11127045	0.89[GIH][hapmap]
rs12614447	0.91[GIH][hapmap]
rs12615285	0.91[GIH][hapmap]
rs12623509	0.80[GIH][hapmap]
rs12714190	0.82[GIH][hapmap]
rs12987172	0.91[GIH][hapmap]
rs13015620	0.91[GIH][hapmap]
rs13034615	0.93[GIH][hapmap]
rs1629293	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs218059	0.84[EUR][1000 genomes]
rs218060	0.81[MEX][hapmap]
rs2241803	0.91[GIH][hapmap]
rs308900	0.85[EUR][1000 genomes]
rs308901	0.82[CHB][hapmap];0.81[MEX][hapmap]
rs308903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs308910	0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs308911	0.81[MEX][hapmap]
rs308912	0.86[EUR][1000 genomes]
rs308914	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs308915	0.87[GIH][hapmap]
rs3201448	0.91[GIH][hapmap]
rs3755002	0.91[GIH][hapmap]
rs396354	0.81[MEX][hapmap]
rs422240	0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4832045	0.87[EUR][1000 genomes]
rs4832046	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4832300	0.91[GIH][hapmap]
rs4832304	0.82[GIH][hapmap]
rs6547700	0.96[CEU][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738663	0.91[GIH][hapmap]
rs6750226	0.91[GIH][hapmap]
rs6752371	0.82[GIH][hapmap]
rs683139	0.81[MEX][hapmap]
rs689912	0.80[EUR][1000 genomes]
rs7584882	0.82[GIH][hapmap]
rs7596717	0.82[GIH][hapmap]
rs9284788	0.91[GIH][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs308902	VPS24	cis	lymphoblastoid	seeQTL
rs308902	C2orf68	cis	cerebellum	SCAN
rs308902	POLR1A	cis	cerebellum	SCAN
rs308902	IMMT	cis	cerebellum	SCAN
rs308902	RNF103	cis	cerebellum	SCAN
rs308902	MAT2A	cis	parietal	SCAN
rs308902	PTCD3	cis	cerebellum	SCAN
rs308902	MRPL35	cis	parietal	SCAN
rs308902	VPS24	cis	parietal	SCAN
rs308902	RMND5A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:86826800-86847800	Weak transcription	NHEK	skin
3	chr2:86828200-86847800	Weak transcription	NHLF	lung
4	chr2:86829000-86845400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:86829400-86848400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:86829400-86849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:86829600-86846200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:86829800-86846000	Weak transcription	NH-A	brain
9	chr2:86829800-86849400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:86830000-86846200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:86830000-86848600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:86830400-86846200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:86830400-86847600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:86830400-86848600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:86830600-86847000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:86830800-86845000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:86830800-86845600	Strong transcription	Dnd41	blood
18	chr2:86830800-86847600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:86830800-86847800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:86830800-86848000	Strong transcription	Placenta	Placenta
21	chr2:86831000-86847200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:86831800-86848000	Weak transcription	HMEC	breast
23	chr2:86831800-86848200	Weak transcription	K562	blood
24	chr2:86832200-86848200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:86832400-86849400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:86832600-86844600	Weak transcription	Fetal Brain Male	brain
27	chr2:86832600-86844600	Weak transcription	Small Intestine	intestine
28	chr2:86832600-86848200	Weak transcription	Colonic Mucosa	Colon
29	chr2:86833000-86848200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:86834000-86846800	Strong transcription	Fetal Lung	lung
31	chr2:86834400-86846600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:86834400-86847000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:86834600-86844600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr2:86834600-86847400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:86834600-86847800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr2:86835200-86847200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:86835200-86847800	Weak transcription	Hela-S3	cervix
38	chr2:86835400-86845200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:86835400-86846600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:86835600-86844000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:86835800-86847200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:86835800-86847600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:86836600-86848600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:86837000-86848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:86837200-86847800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:86838000-86846800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:86838400-86845000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:86839000-86847400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:86839400-86847400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:86839600-86847600	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links