Variant report

Variant	rs4756803
Chromosome Location	chr11:15250926-15250927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10766213	0.94[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10766214	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10766215	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10766216	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832372	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832373	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832374	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832375	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832376	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10832377	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11023471	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11023472	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11828254	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1945626	0.84[ASN][1000 genomes]
rs1945629	0.92[CHB][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1945630	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4756800	0.82[CHD][hapmap];1.00[MEX][hapmap]
rs4756802	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4757298	0.82[CHD][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs4757299	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4757300	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4757301	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5004266	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7129739	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs939049	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs939051	0.83[CEU][hapmap];0.93[CHB][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897007	chr11:14991411-15260124	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv530217	chr11:14991411-15275034	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2830370	chr11:15142247-15444094	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv897010	chr11:15219258-15279421	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv832072	chr11:15226843-15392190	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv975323	chr11:15249916-15262360	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4756803	SPTY2D1	cis	parietal	SCAN
rs4756803	SAA4	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:15234400-15272000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr11:15242000-15269000	Weak transcription	Pancreas	Pancrea
3	chr11:15245000-15271200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr11:15245400-15259600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:15246800-15254200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:15248000-15252200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:15250400-15251200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:15250400-15251200	Enhancers	Osteobl	bone
9	chr11:15250400-15252200	Weak transcription	Fetal Stomach	stomach
10	chr11:15250600-15254800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr11:15250600-15261800	Weak transcription	Aorta	Aorta

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