Variant report

Variant	rs6919257
Chromosome Location	chr6:56113300-56113301
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000124749	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12110798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1925140	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[ASN][1000 genomes]
rs2147696	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2397211	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2894834	0.90[ASN][1000 genomes]
rs60407790	0.90[ASN][1000 genomes]
rs62411896	0.95[ASN][1000 genomes]
rs6459141	0.95[ASN][1000 genomes]
rs6902532	0.95[ASN][1000 genomes]
rs6904902	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6905216	0.95[ASN][1000 genomes]
rs6920090	0.95[ASN][1000 genomes]
rs6923130	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[ASN][1000 genomes]
rs6925652	0.81[TSI][hapmap]
rs6931235	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6931381	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7753541	0.95[ASN][1000 genomes]
rs7757732	0.95[ASN][1000 genomes]
rs7760380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[ASN][1000 genomes]
rs9296835	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9296837	0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs9464368	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9464370	0.95[ASN][1000 genomes]
rs9475643	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9475645	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9475647	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs9475649	0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6919257	COL21A1	cis	cerebellum	SCAN
rs6919257	LRRC1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56112400-56113400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:56112800-56115200	Weak transcription	Lung	lung
3	chr6:56112800-56115200	Weak transcription	Pancreas	Pancrea
4	chr6:56112800-56116600	Weak transcription	Psoas Muscle	Psoas
5	chr6:56113000-56113400	Enhancers	H9 Cell Line	embryonic stem cell
6	chr6:56113000-56114800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:56113000-56120200	Weak transcription	Aorta	Aorta
8	chr6:56113200-56113400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr6:56113200-56113400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr6:56113200-56113400	Flanking Active TSS	Rectal Smooth Muscle	rectum
11	chr6:56113200-56114200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:56113200-56117000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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