Variant report

Variant	rs5015480
Chromosome Location	chr10:94465559-94465560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10882098	0.97[EUR][1000 genomes]
rs10882099	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10882101	1.00[EUR][1000 genomes]
rs10882102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1111875	0.99[EUR][1000 genomes]
rs11187138	1.00[EUR][1000 genomes]
rs11187139	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11187144	0.88[AFR][1000 genomes]
rs12219514	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12778642	0.94[EUR][1000 genomes]
rs1977832	0.99[EUR][1000 genomes]
rs1977833	0.99[EUR][1000 genomes]
rs35906730	0.83[EUR][1000 genomes]
rs7087591	0.89[ASW][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs7903302	0.84[EUR][1000 genomes]
rs7923837	0.86[JPT][hapmap]
rs7923866	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	esv3446249	chr10:94374508-94549394	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv1794949	chr10:94392728-94465559	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv825517	chr10:94397149-94472509	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv825518	chr10:94403446-94467700	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

Variant related diseases (count:5)

Disease	PMID	Source
Type 2 diabetes	20581827	GWAS catalog
Type 2 diabetes	18372903	GWAS catalog
Type 2 diabetes	17463249	GWAS catalog
Type 2 diabetes	20862305	GWAS catalog
Type 2 diabetes	22693455	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5015480	KIF11	cis	cerebellum	SCAN
rs5015480	ROD1	trans	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94459800-94474000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:94462400-94473400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:94463200-94465800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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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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