Variant report

Variant	rs1661409
Chromosome Location	chr11:101775663-101775664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1004352	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791545	0.87[CHB][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10895220	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895228	0.82[EUR][1000 genomes]
rs10895231	0.87[CHB][hapmap]
rs11225049	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11225080	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11225093	0.87[CHB][hapmap]
rs12281520	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12787877	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12802591	0.87[CHB][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs1372414	0.87[CHB][hapmap];0.81[GIH][hapmap]
rs1441929	0.87[CHB][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs1661410	0.90[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1661411	0.87[CHB][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs1783740	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119734	0.87[CHB][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2282612	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59927719	0.93[ASN][1000 genomes]
rs6590941	0.87[CHB][hapmap]
rs7105709	0.81[TSI][hapmap]
rs7107662	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7122772	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs975810	0.87[CHB][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][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	nsv1052159	chr11:101439655-101853293	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1051457	chr11:101446705-101837650	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv530645	chr11:101451416-101778666	Bivalent/Poised TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv832250	chr11:101617934-101804020	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1661409	KIAA1377	cis	cerebellum	SCAN
rs1661409	KIAA1377	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101750200-101778200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:101774600-101776000	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr11:101775600-101775800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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