Variant report

Variant	rs16986509
Chromosome Location	chr22:28943477-28943478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28934195..28936559-chr22:28940613..28943481,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10222318	0.81[AFR][1000 genomes]
rs10483151	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12165708	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12165715	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs12165893	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs12166129	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12166245	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs12166363	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12166475	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs12167667	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12168765	0.90[CEU][hapmap]
rs12169120	0.86[AMR][1000 genomes]
rs12169262	0.91[CEU][hapmap];0.95[YRI][hapmap]
rs12169460	0.91[CEU][hapmap]
rs12169595	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12169966	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs134506	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs134514	0.91[CEU][hapmap];0.88[MEX][hapmap];0.83[YRI][hapmap]
rs134524	0.91[CEU][hapmap]
rs134547	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs1474961	0.91[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16986398	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs17413461	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17507066	0.91[CEU][hapmap]
rs2013784	0.91[CEU][hapmap]
rs2144922	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs55738739	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57871917	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs58542867	0.84[AMR][1000 genomes]
rs58579082	0.89[AFR][1000 genomes]
rs59262169	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60042154	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6005807	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60065194	0.84[AMR][1000 genomes]
rs6519753	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7289534	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs7289625	0.91[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs7291268	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7293232	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs73430105	0.90[AFR][1000 genomes]
rs73430123	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73430136	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73430155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73430163	0.92[AFR][1000 genomes]
rs73430168	0.88[AFR][1000 genomes]
rs73430179	0.84[AMR][1000 genomes]
rs73430186	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73430189	0.86[AMR][1000 genomes]
rs73430202	0.89[AFR][1000 genomes]
rs73437900	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73439811	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs738200	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs738627	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8137200	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8137808	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9306457	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9608696	0.91[CEU][hapmap]
rs9620797	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620799	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620803	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620804	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620808	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs9620809	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620810	0.91[CEU][hapmap]
rs9620811	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs9620817	0.81[CEU][hapmap]
rs9625467	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625475	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625478	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625481	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625484	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9625487	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625492	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625498	0.84[AMR][1000 genomes]
rs9625501	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625508	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625509	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9625510	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9625512	0.91[CEU][hapmap]
rs9625513	0.91[CEU][hapmap]
rs9625514	0.84[CEU][hapmap]
rs9625515	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625516	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9625520	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs9625521	0.91[CEU][hapmap]
rs9625522	0.91[CEU][hapmap]
rs9625523	0.91[CEU][hapmap]
rs9625524	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs9625534	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16986509	TTC28	cis	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28933600-28953800	Weak transcription	HSMMtube	muscle
2	chr22:28937000-28945600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:28937400-28950800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:28937600-28946200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr22:28937600-28946400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr22:28939400-28943800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr22:28939600-28944200	Weak transcription	Fetal Lung	lung
8	chr22:28939600-28946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr22:28942800-28944000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr22:28942800-28944400	Enhancers	Osteobl	bone
11	chr22:28942800-28944600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr22:28942800-28944600	Enhancers	Fetal Brain Female	brain
13	chr22:28943000-28943800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:28943000-28944600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr22:28943000-28944600	Enhancers	NHDF-Ad	bronchial
16	chr22:28943000-28944600	Enhancers	NHLF	lung
17	chr22:28943000-28944800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr22:28943000-28945800	Enhancers	Fetal Brain Male	brain
19	chr22:28943200-28943600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr22:28943200-28943600	Enhancers	Rectal Smooth Muscle	rectum
21	chr22:28943200-28944400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:28943200-28944600	Enhancers	Hela-S3	cervix
23	chr22:28943400-28943600	Weak transcription	Left Ventricle	heart
24	chr22:28943400-28943800	Flanking Active TSS	A549	lung
25	chr22:28943400-28944400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr22:28943400-28944400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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