Variant report

Variant	rs2515192
Chromosome Location	chr8:104032173-104032174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr8:104032059-104032253	SH-SY5Y	brain:	n/a	chr8:104032104-104032113
2	POLR2A	chr8:104032131-104032241	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:103873561..103877987-chr8:104030387..104035295,15	K562	blood:
2	chr8:103875552..103877856-chr8:104031071..104034645,4	K562	blood:
3	chr8:103874643..103878099-chr8:104031324..104040310,20	MCF-7	breast:
4	chr8:104031977..104033590-chr8:104309490..104311650,2	MCF-7	breast:
5	chr8:104026806..104029489-chr8:104031161..104032899,2	K562	blood:
6	chr8:104027811..104029796-chr8:104031590..104033402,2	MCF-7	breast:
7	chr8:104026806..104029489-chr8:104031161..104033140,3	K562	blood:
8	chr8:103936608..103938218-chr8:104032062..104033919,2	MCF-7	breast:
9	chr8:103870045..103872985-chr8:104031865..104034556,2	MCF-7	breast:
10	chr8:103873594..103879966-chr8:104029090..104036191,28	MCF-7	breast:
11	chr8:104032077..104034821-chr8:104426211..104427812,2	MCF-7	breast:
12	chr8:104024663..104026547-chr8:104030749..104032308,2	MCF-7	breast:
13	chr17:62222917..62224705-chr8:104031776..104034703,2	MCF-7	breast:

No data

Variant related genes	Relation type
ATP6V1C1	TF binding region
ENSG00000266402	Chromatin interaction
ENSG00000247081	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000164933	Chromatin interaction
ENSG00000253663	Chromatin interaction
ENSG00000164934	Chromatin interaction
ENSG00000164930	Chromatin interaction
ENSG00000155096	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1512348	0.82[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs1566158	0.82[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs1849339	0.86[CHB][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2047378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2048549	0.87[JPT][hapmap]
rs2048550	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]
rs2458272	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2515174	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2515180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2515194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3019163	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[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];0.99[ASN][1000 genomes]
rs515024	0.82[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap]
rs55801214	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs575524	0.82[CEU][hapmap]
rs600667	0.83[GIH][hapmap]
rs7013362	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7816151	0.85[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2515192	BAALC	cis	parietal	SCAN
rs2515192	BAALC	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104023200-104032800	Weak transcription	Pancreas	Pancrea
2	chr8:104031600-104032400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr8:104031800-104032800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr8:104032000-104032200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr8:104032000-104032200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:104032000-104032200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr8:104032000-104032200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr8:104032000-104032200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr8:104032000-104032200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr8:104032000-104032200	Enhancers	K562	blood
11	chr8:104032000-104032400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr8:104032000-104032400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr8:104032000-104032600	Active TSS	Primary T helper cells fromperipheralblood	blood

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