Variant report

Variant	rs17412920
Chromosome Location	chr22:28834531-28834532
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	chr22:28828789..28831593-chr22:28834204..28836919,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10427676	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs134527	0.95[JPT][hapmap]
rs134544	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17504822	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2056962	1.00[ASW][hapmap]
rs2223369	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs2346395	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs5752728	0.94[ASN][1000 genomes]
rs5752729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752745	0.85[CEU][hapmap]
rs5752746	0.94[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs5752766	0.89[EUR][1000 genomes]
rs5762572	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762604	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762659	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5762664	1.00[LWK][hapmap]
rs5762666	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762686	1.00[ASW][hapmap];0.84[CEU][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs5762736	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs695388	0.90[JPT][hapmap]
rs7286920	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7288416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168176	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs738199	0.85[CEU][hapmap]
rs738995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs738996	1.00[ASW][hapmap]
rs9306454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs9306455	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9306458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9608677	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs9608692	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9613609	0.98[ASN][1000 genomes]
rs9613617	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613639	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9613658	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17412920	C22orf13	cis	parietal	SCAN
rs17412920	CABP7	cis	cerebellum	SCAN
rs17412920	MTFP1	cis	cerebellum	SCAN
rs17412920	TTC28	cis	cerebellum	SCAN
rs17412920	TFIP11	cis	cerebellum	SCAN

Chromatin state (count:46 , 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	chr22:28827200-28836200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr22:28827200-28836200	Weak transcription	Brain Germinal Matrix	brain
8	chr22:28827200-28836400	Weak transcription	Brain Anterior Caudate	brain
9	chr22:28827200-28836400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr22:28827200-28837400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr22:28829400-28834800	Weak transcription	Osteobl	bone
12	chr22:28829400-28837600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr22:28831000-28836400	Weak transcription	Aorta	Aorta
14	chr22:28831800-28836400	Weak transcription	Brain Substantia Nigra	brain
15	chr22:28832000-28836400	Weak transcription	Liver	Liver
16	chr22:28832200-28836400	Weak transcription	Adipose Nuclei	Adipose
17	chr22:28832400-28834600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr22:28832400-28836200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr22:28832400-28836400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr22:28832400-28836400	Weak transcription	NHLF	lung
21	chr22:28832400-28836600	Weak transcription	Fetal Heart	heart
22	chr22:28832400-28837000	Weak transcription	Small Intestine	intestine
23	chr22:28832600-28836000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr22:28832600-28836000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr22:28832600-28836200	Weak transcription	NHDF-Ad	bronchial
26	chr22:28832600-28836800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr22:28832800-28835400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr22:28832800-28837800	Weak transcription	HMEC	breast
29	chr22:28833400-28835800	Flanking Active TSS	Dnd41	blood
30	chr22:28833400-28840000	Active TSS	Fetal Brain Female	brain
31	chr22:28833600-28834800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr22:28833600-28835000	Enhancers	Fetal Lung	lung
33	chr22:28833600-28837600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr22:28833800-28837600	Weak transcription	Right Atrium	heart
35	chr22:28833800-28838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr22:28833800-28838000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr22:28834000-28835200	Weak transcription	Ovary	ovary
38	chr22:28834000-28836400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr22:28834000-28836600	Weak transcription	Fetal Kidney	kidney
40	chr22:28834000-28837600	Weak transcription	NHEK	skin
41	chr22:28834000-28837800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr22:28834000-28837800	Weak transcription	Psoas Muscle	Psoas
43	chr22:28834200-28834800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr22:28834200-28835000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr22:28834400-28834800	Flanking Active TSS	Fetal Brain Male	brain
46	chr22:28834400-28835400	Weak transcription	Colon Smooth Muscle	Colon

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