Variant report

Variant	rs10896488
Chromosome Location	chr11:56344260-56344261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10896484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10896486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10896494	0.84[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs10896495	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10896498	0.84[ASN][1000 genomes]
rs11228647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11228675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11228685	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11228697	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11228699	0.83[AMR][1000 genomes]
rs11228704	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11228705	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11228717	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12225008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12365813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1397054	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1510004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4938829	1.00[ASW][hapmap];0.85[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs4938835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs4939046	0.81[CHB][hapmap]
rs4939079	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs605734	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs611459	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs624412	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs638801	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs640953	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs652537	0.81[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs675991	1.00[ASW][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs72915700	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7930678	0.81[CHB][hapmap]
rs7931261	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050024	chr11:55900482-56518943	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
2	nsv497854	chr11:55917298-56537994	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv468576	chr11:56299930-56420029	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv555099	chr11:56299930-56420029	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv516558	chr11:56315297-56347636	Weak transcription Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
6	esv2421725	chr11:56323407-56354044	Enhancers Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv523453	chr11:56324576-56366677	Enhancers Weak transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
8	nsv525637	chr11:56330546-56366677	Weak transcription Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
9	nsv1037096	chr11:56332750-56380919	Enhancers Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2760201	chr11:56332762-56368515	Weak transcription Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
11	nsv971950	chr11:56344170-56345170	Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10896488	SLC43A1	cis	parietal	SCAN
rs10896488	DTX4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56342200-56345000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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