Variant report

Variant	rs10896596
Chromosome Location	chr11:57020516-57020517
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10732882	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs10792083	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10792085	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10896601	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896602	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11228971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11228988	0.85[ASN][1000 genomes]
rs11602501	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11604373	0.82[ASN][1000 genomes]
rs17573746	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1939496	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2155231	0.88[EUR][1000 genomes]
rs2282623	0.82[YRI][hapmap]
rs2511026	0.84[EUR][1000 genomes]
rs2511029	0.93[EUR][1000 genomes]
rs2846049	0.83[EUR][1000 genomes]
rs2846051	0.92[EUR][1000 genomes]
rs3935069	0.91[ASN][1000 genomes]
rs4939129	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4939131	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4939134	0.82[AFR][1000 genomes]
rs5012051	1.00[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs522656	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs590240	0.94[EUR][1000 genomes]
rs7130020	0.85[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs746886	0.82[YRI][hapmap]
rs7928905	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7931298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7936545	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7943761	0.85[ASN][1000 genomes]
rs7943915	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7948723	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv482317	chr11:56857026-57028631	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10896596	OR5M9	cis	cerebellum	SCAN
rs10896596	OR9I1	cis	cerebellum	SCAN
rs10896596	OR4C6	cis	parietal	SCAN
rs10896596	GLYATL2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57016400-57020800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:57016400-57020800	Enhancers	HMEC	breast
3	chr11:57017000-57021000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:57017000-57021000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:57017200-57023200	Weak transcription	HSMMtube	muscle
6	chr11:57017200-57026000	Weak transcription	Fetal Brain Male	brain
7	chr11:57018000-57021200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:57018200-57028800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:57019600-57021600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:57019600-57022200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:57019600-57022800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:57019600-57022800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:57020200-57020800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:57020200-57021000	Enhancers	NHEK	skin
15	chr11:57020400-57020600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr11:57020400-57020800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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