Variant report

Variant	rs6903211
Chromosome Location	chr6:56306281-56306282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10484787	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]
rs1323318	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1323319	0.91[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16887916	0.98[EUR][1000 genomes]
rs2209037	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2224749	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2397225	1.00[EUR][1000 genomes]
rs56199254	1.00[ASN][1000 genomes]
rs6915066	0.85[CEU][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6917087	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs6941846	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs73745839	1.00[ASN][1000 genomes]
rs9475698	0.85[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6903211	VPS28	trans	cerebellum	SCAN
rs6903211	COL21A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56303200-56309600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:56304200-56314800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:56304400-56307200	Enhancers	Fetal Intestine Large	intestine
4	chr6:56304800-56307400	Enhancers	Fetal Intestine Small	intestine
5	chr6:56304800-56309600	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:56305000-56307400	Enhancers	Liver	Liver
7	chr6:56305600-56313000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:56305600-56315800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:56305600-56318600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:56305600-56319600	Weak transcription	HMEC	breast
11	chr6:56305800-56309600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:56306000-56306800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:56306000-56309000	Weak transcription	Pancreas	Pancrea

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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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