Variant report

Variant	rs10484787
Chromosome Location	chr6:56304291-56304292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56295799..56298000-chr6:56302478..56305117,2	MCF-7	breast:
2	chr6:56302994..56305596-chr6:56305706..56307687,2	MCF-7	breast:
3	chr6:56298843..56301958-chr6:56302177..56305032,4	MCF-7	breast:
4	chr6:56242114..56244288-chr6:56303044..56304750,2	MCF-7	breast:
5	chr6:56243942..56247033-chr6:56303376..56305321,3	MCF-7	breast:
6	chr6:56302783..56304567-chr6:56307682..56311074,3	K562	blood:
7	chr6:56303405..56305333-chr6:56316086..56317917,2	MCF-7	breast:
8	chr6:56300059..56302914-chr6:56304069..56306007,3	MCF-7	breast:
9	chr6:56302272..56304298-chr6:56305503..56307408,2	K562	blood:
10	chr6:56302630..56305077-chr6:56407760..56410392,2	MCF-7	breast:
11	chr6:56302578..56305844-chr6:56326114..56330070,4	MCF-7	breast:
12	chr6:56303118..56304788-chr6:56406546..56408135,2	MCF-7	breast:
13	chr6:56247738..56250356-chr6:56304271..56306407,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1323318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323319	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715633	1.00[CHB][hapmap]
rs56199254	1.00[ASN][1000 genomes]
rs6903211	0.92[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6915066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917087	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6941846	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73465822	1.00[EUR][1000 genomes]
rs73745839	1.00[ASN][1000 genomes]
rs9475698	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10484787	COL21A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56301000-56304400	Weak transcription	Fetal Intestine Large	intestine
2	chr6:56301000-56305200	Weak transcription	Pancreas	Pancrea
3	chr6:56302800-56305000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:56303000-56304400	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:56303000-56304800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:56303000-56305000	Weak transcription	Stomach Mucosa	stomach
7	chr6:56303000-56305200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:56303200-56309600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:56303600-56304400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:56304000-56304400	Enhancers	Liver	Liver
11	chr6:56304200-56305200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:56304200-56314800	Weak transcription	Muscle Satellite Cultured Cells	--

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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