Variant report

Variant	rs695388
Chromosome Location	chr22:28833502-28833503
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs134522	0.85[CEU][hapmap]
rs134527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs134529	0.82[CEU][hapmap]
rs134544	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs134545	0.85[CEU][hapmap]
rs17412920	0.90[JPT][hapmap]
rs5752729	0.85[JPT][hapmap]
rs5752746	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5762622	0.85[JPT][hapmap]
rs5762654	0.90[JPT][hapmap]
rs5762656	0.85[JPT][hapmap]
rs5762668	0.81[EUR][1000 genomes]
rs5762670	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs6005754	0.85[CEU][hapmap]
rs6005790	0.85[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs695318	0.82[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap]
rs695567	0.85[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs695629	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs695700	0.85[CEU][hapmap]
rs695709	0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7288416	0.85[JPT][hapmap]
rs7289516	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs737622	0.81[CEU][hapmap]
rs738995	0.90[JPT][hapmap]
rs9306454	0.95[JPT][hapmap]
rs9306458	1.00[JPT][hapmap]
rs9613609	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9613617	0.90[JPT][hapmap]
rs9613630	0.85[JPT][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	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	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
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs695388	TTC28	cis	lymphoblastoid	seeQTL
rs695388	TTC28	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28820800-28837400	Weak transcription	HSMMtube	muscle
2	chr22:28821400-28836600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr22:28822200-28837800	Weak transcription	Left Ventricle	heart
4	chr22:28823000-28837000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr22:28827000-28837000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr22:28827200-28833600	Weak transcription	Psoas Muscle	Psoas
7	chr22:28827200-28836200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr22:28827200-28836200	Weak transcription	Brain Germinal Matrix	brain
9	chr22:28827200-28836400	Weak transcription	Brain Anterior Caudate	brain
10	chr22:28827200-28836400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr22:28827200-28837400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr22:28827400-28834200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr22:28829400-28834800	Weak transcription	Osteobl	bone
14	chr22:28829400-28837600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr22:28831000-28836400	Weak transcription	Aorta	Aorta
16	chr22:28831200-28833600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr22:28831400-28834000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr22:28831800-28834000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:28831800-28836400	Weak transcription	Brain Substantia Nigra	brain
20	chr22:28832000-28833600	Weak transcription	Fetal Lung	lung
21	chr22:28832000-28836400	Weak transcription	Liver	Liver
22	chr22:28832200-28836400	Weak transcription	Adipose Nuclei	Adipose
23	chr22:28832400-28833800	Weak transcription	Colon Smooth Muscle	Colon
24	chr22:28832400-28834600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr22:28832400-28836200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr22:28832400-28836400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr22:28832400-28836400	Weak transcription	NHLF	lung
28	chr22:28832400-28836600	Weak transcription	Fetal Heart	heart
29	chr22:28832400-28837000	Weak transcription	Small Intestine	intestine
30	chr22:28832600-28833600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr22:28832600-28836000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr22:28832600-28836000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:28832600-28836200	Weak transcription	NHDF-Ad	bronchial
34	chr22:28832600-28836800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr22:28832800-28835400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr22:28832800-28837800	Weak transcription	HMEC	breast
37	chr22:28833000-28833800	Enhancers	Fetal Brain Male	brain
38	chr22:28833200-28833600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr22:28833200-28834000	Enhancers	NHEK	skin
40	chr22:28833400-28834000	Enhancers	Fetal Kidney	kidney
41	chr22:28833400-28834000	Enhancers	Ovary	ovary
42	chr22:28833400-28835800	Flanking Active TSS	Dnd41	blood
43	chr22:28833400-28840000	Active TSS	Fetal Brain Female	brain

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