Variant report

Variant	rs9620778
Chromosome Location	chr22:28620584-28620585
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10154425	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs10212083	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10483143	1.00[ASW][hapmap];0.88[MEX][hapmap]
rs12166023	0.81[CEU][hapmap]
rs12166077	0.93[GIH][hapmap];0.88[MEX][hapmap]
rs12166253	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12166719	0.90[YRI][hapmap]
rs12166740	0.81[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap]
rs12166912	0.81[CEU][hapmap]
rs12167735	1.00[ASW][hapmap];0.81[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12168180	0.81[CEU][hapmap]
rs12168652	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12168708	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12168851	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12170637	0.91[CEU][hapmap]
rs1297607	0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs134194	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs134197	0.91[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs134488	0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs134506	0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs134514	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs134524	0.91[CEU][hapmap]
rs134547	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs138642	0.80[AMR][1000 genomes]
rs16985967	1.00[ASW][hapmap];0.88[MEX][hapmap]
rs16986037	1.00[ASW][hapmap];0.81[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap]
rs16986077	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[MEX][hapmap]
rs16986398	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs16987005	0.81[CEU][hapmap]
rs17483887	1.00[ASW][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap]
rs17487463	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2143420	1.00[ASW][hapmap]
rs2345717	0.84[AMR][1000 genomes]
rs28579300	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs55846737	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56391942	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58936636	0.84[AFR][1000 genomes]
rs738200	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs73882704	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73882705	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73882709	0.84[AMR][1000 genomes]
rs73882711	0.84[AFR][1000 genomes]
rs9306452	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs9620764	0.93[GIH][hapmap];0.88[MEX][hapmap]
rs9620768	0.81[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap]
rs9620769	1.00[ASW][hapmap];0.81[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap]
rs9620770	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs9620779	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625391	1.00[ASW][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap]
rs9625395	0.81[CEU][hapmap]
rs9625413	0.81[CEU][hapmap]
rs9625416	0.81[CEU][hapmap]
rs9625417	0.81[CEU][hapmap]
rs9625425	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9625427	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9625430	0.80[AMR][1000 genomes]
rs9625433	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625437	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9625438	0.91[CEU][hapmap]
rs9625440	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625441	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9625447	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625467	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs988893	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9620778	TTC28	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28612200-28625600	Weak transcription	Aorta	Aorta
2	chr22:28612200-28634800	Weak transcription	Dnd41	blood
3	chr22:28615800-28626400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr22:28617400-28625400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr22:28617600-28626200	Weak transcription	Psoas Muscle	Psoas
6	chr22:28617800-28620800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr22:28618000-28620600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr22:28618400-28626800	Weak transcription	Fetal Kidney	kidney
9	chr22:28618400-28639600	Weak transcription	Ovary	ovary
10	chr22:28618400-28662200	Weak transcription	Pancreas	Pancrea
11	chr22:28619000-28626000	Weak transcription	Colon Smooth Muscle	Colon
12	chr22:28619200-28621000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr22:28619200-28626400	Weak transcription	Fetal Lung	lung
14	chr22:28619400-28625600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr22:28619400-28631000	Weak transcription	Brain Hippocampus Middle	brain
16	chr22:28620000-28620600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr22:28620000-28625200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr22:28620200-28625000	Weak transcription	Osteobl	bone
19	chr22:28620200-28625200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr22:28620200-28625400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr22:28620400-28625200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:28620400-28625200	Weak transcription	NHDF-Ad	bronchial
23	chr22:28620400-28625400	Weak transcription	NHLF	lung
24	chr22:28620400-28625600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:28620400-28625600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr22:28620400-28625600	Weak transcription	Fetal Muscle Leg	muscle
27	chr22:28620400-28626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr22:28620400-28639200	Weak transcription	Left Ventricle	heart

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