Variant report

Variant	rs1925158
Chromosome Location	chr6:56114655-56114656
allele	A/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	STAT3	chr6:56114642-56114777	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56109021..56112703-chr6:56113048..56115800,3	MCF-7	breast:

Variant related genes	Relation type
COL21A1	TF binding region
ENSG00000124749	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10498810	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10948981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12525967	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12530020	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1925160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1925163	0.82[CHD][hapmap]
rs1925187	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1925188	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs2328693	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2397210	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2397212	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2397213	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3807013	0.83[JPT][hapmap]
rs3846927	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846929	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4119562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4119563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4712121	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4715602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4715603	0.84[CHB][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55734123	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67454631	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7745111	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759570	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9349807	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9382597	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9382598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9382599	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9382601	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382603	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382604	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9396185	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs994039	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs994040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1925158	KLHL31	cis	parietal	SCAN
rs1925158	TRAM2	cis	parietal	SCAN
rs1925158	COL21A1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56112800-56115200	Weak transcription	Lung	lung
2	chr6:56112800-56115200	Weak transcription	Pancreas	Pancrea
3	chr6:56112800-56116600	Weak transcription	Psoas Muscle	Psoas
4	chr6:56113000-56114800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:56113000-56120200	Weak transcription	Aorta	Aorta
6	chr6:56113200-56117000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:56113400-56115000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:56113400-56116600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:56113400-56116800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:56113400-56123800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:56113600-56117200	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links