Variant report

Variant	rs1111875
Chromosome Location	chr10:94462882-94462883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10509645	0.85[CHB][hapmap]
rs10882095	0.84[CHB][hapmap]
rs10882098	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882101	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882102	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11187096	0.81[CHB][hapmap]
rs11187114	0.84[CHB][hapmap]
rs11187138	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11187139	0.98[EUR][1000 genomes]
rs12219514	0.92[EUR][1000 genomes]
rs12778642	0.93[EUR][1000 genomes]
rs1977832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421943	0.81[CHB][hapmap]
rs35906730	0.83[EUR][1000 genomes]
rs3824735	0.85[CHB][hapmap]
rs5015480	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7903302	0.84[EUR][1000 genomes]

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:6)

Disease	PMID	Source
Type 2 diabetes	19401414	GWAS catalog
Type 2 diabetes	17463246	GWAS catalog
Type 2 diabetes	24509480	GWAS catalog
Type 2 diabetes	17463248	GWAS catalog
Type 2 diabetes	23945395	GWAS catalog
Type 2 diabetes	17293876	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1111875	ROD1	trans	parietal	SCAN
rs1111875	KIF11	cis	cerebellum	SCAN

Chromatin state (count:12 , 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	chr10:94460000-94463000	Enhancers	Primary B cells from peripheral blood	blood
3	chr10:94460200-94463200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr10:94462000-94463000	Enhancers	K562	blood
5	chr10:94462200-94463000	Enhancers	A549	lung
6	chr10:94462200-94463000	Enhancers	HUVEC	blood vessel
7	chr10:94462400-94463000	Enhancers	Primary hematopoietic stem cells	blood
8	chr10:94462400-94473400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr10:94462600-94463000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr10:94462600-94463000	Enhancers	Dnd41	blood
11	chr10:94462600-94463000	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr10:94462600-94463200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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