Variant report

Variant	rs11654879
Chromosome Location	chr17:66575761-66575762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11077624	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11649763	0.82[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11649965	0.85[CHD][hapmap]
rs11651150	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11654873	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11655376	0.80[CHB][hapmap]
rs11656128	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744506	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59183747	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59251979	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60871479	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67127022	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67717905	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67810719	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67844728	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68005369	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7222228	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8082354	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833524	chr17:66524030-66705194	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11654879	FAM20A	cis	multi-tissue	Pritchard
rs11654879	AXIN2	cis	cerebellum	SCAN
rs11654879	Contig34504_RC	trans	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66538800-66575800	Weak transcription	Spleen	Spleen
2	chr17:66539200-66588000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:66551800-66587800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr17:66552000-66584200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr17:66552000-66585200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr17:66571200-66578000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:66571400-66575800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr17:66572000-66578400	Enhancers	NHDF-Ad	bronchial
9	chr17:66572200-66577600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:66572200-66591800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:66572400-66577400	Enhancers	Adipose Nuclei	Adipose
12	chr17:66572600-66576000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:66572600-66581200	Weak transcription	Gastric	stomach
14	chr17:66572800-66576000	Weak transcription	Lung	lung
15	chr17:66572800-66582800	Weak transcription	Brain Angular Gyrus	brain
16	chr17:66573400-66576000	Weak transcription	Colon Smooth Muscle	Colon
17	chr17:66573400-66577200	Weak transcription	NHLF	lung
18	chr17:66573600-66576000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:66573600-66578000	Weak transcription	Right Atrium	heart
20	chr17:66573800-66578200	Weak transcription	Placenta	Placenta
21	chr17:66574000-66575800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:66574000-66576600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr17:66574600-66576000	Enhancers	HepG2	liver
24	chr17:66574800-66575800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr17:66575000-66576200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr17:66575200-66576800	Flanking Active TSS	Liver	Liver
27	chr17:66575200-66577200	Enhancers	Fetal Thymus	thymus
28	chr17:66575200-66577400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr17:66575400-66575800	Enhancers	Osteobl	bone
30	chr17:66575400-66576000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:66575400-66576800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr17:66575400-66577000	Enhancers	Esophagus	oesophagus
33	chr17:66575400-66577200	Enhancers	Ovary	ovary
34	chr17:66575600-66575800	Enhancers	Fetal Lung	lung
35	chr17:66575600-66576000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
36	chr17:66575600-66577400	Bivalent Enhancer	Fetal Muscle Leg	muscle

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