Variant report

Variant	rs1543416
Chromosome Location	chr22:31925073-31925074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11704494	0.83[AFR][1000 genomes]
rs12170867	0.81[JPT][hapmap]
rs12171042	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs12484606	0.89[EUR][1000 genomes]
rs12485048	0.86[CHB][hapmap]
rs13056823	0.90[EUR][1000 genomes]
rs1916	0.85[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs2006771	0.86[YRI][hapmap]
rs2012451	0.85[LWK][hapmap]
rs2024747	0.86[JPT][hapmap]
rs2092905	0.81[JPT][hapmap]
rs2295242	0.81[JPT][hapmap]
rs2295251	0.95[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap]
rs2387	0.81[JPT][hapmap]
rs3818134	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4535154	0.88[EUR][1000 genomes]
rs4820048	0.87[LWK][hapmap];0.86[YRI][hapmap]
rs4820974	0.87[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs4820976	0.88[EUR][1000 genomes]
rs4820978	0.92[EUR][1000 genomes]
rs4820979	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs4820980	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs4820981	0.88[EUR][1000 genomes]
rs4820982	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749286	0.82[JPT][hapmap]
rs5749287	0.87[EUR][1000 genomes]
rs5749293	0.86[JPT][hapmap]
rs5749298	0.82[JPT][hapmap]
rs5749303	0.81[JPT][hapmap]
rs5749304	0.84[ASW][hapmap];0.82[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs5749306	0.81[JPT][hapmap]
rs5753659	0.82[JPT][hapmap]
rs5753667	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs5753669	0.82[JPT][hapmap]
rs5753671	0.82[JPT][hapmap]
rs5753680	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753681	0.86[JPT][hapmap]
rs5753686	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753734	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs5997971	0.83[YRI][hapmap]
rs5997988	0.85[LWK][hapmap]
rs5998002	0.90[LWK][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs5998011	0.89[EUR][1000 genomes]
rs5998032	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5998035	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5998042	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5998054	0.82[TSI][hapmap]
rs6518745	0.82[LWK][hapmap]
rs7284622	0.82[JPT][hapmap]
rs7287937	0.82[YRI][hapmap]
rs7289075	1.00[CEU][hapmap]
rs7291918	0.89[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap]
rs738656	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs738702	0.81[JPT][hapmap]
rs761746	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs8461	0.85[GIH][hapmap]
rs926928	0.82[LWK][hapmap]
rs9606848	0.82[JPT][hapmap]
rs9609296	0.82[JPT][hapmap]
rs9609297	0.82[JPT][hapmap]
rs9609304	0.82[JPT][hapmap]
rs9621279	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9956	0.94[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][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	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1059314	chr22:31893613-31936088	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv914978	chr22:31897795-31942770	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1543416	SFI1	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31893200-31934800	Weak transcription	Ovary	ovary
2	chr22:31893400-31971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr22:31893600-31925600	Weak transcription	Gastric	stomach
4	chr22:31893600-31926200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr22:31893600-31928200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr22:31893600-31934800	Weak transcription	Pancreas	Pancrea
7	chr22:31893600-31946600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr22:31893600-31970000	Weak transcription	Colonic Mucosa	Colon
9	chr22:31893800-31925200	Weak transcription	Brain Hippocampus Middle	brain
10	chr22:31893800-31925400	Weak transcription	Brain Angular Gyrus	brain
11	chr22:31893800-31925600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr22:31893800-31926400	Weak transcription	Fetal Lung	lung
13	chr22:31893800-31927000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr22:31893800-31934800	Weak transcription	HMEC	breast
15	chr22:31893800-31945600	Weak transcription	Brain Anterior Caudate	brain
16	chr22:31894000-31926400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr22:31894000-31946600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr22:31894000-31946600	Weak transcription	Fetal Brain Female	brain
19	chr22:31895400-31931200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr22:31898000-31934800	Weak transcription	Spleen	Spleen
21	chr22:31900200-31926400	Weak transcription	HSMM	muscle
22	chr22:31900800-31940800	Weak transcription	NHEK	skin
23	chr22:31901000-31926200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr22:31901000-31926400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr22:31901800-31926000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr22:31903400-31934400	Weak transcription	Hela-S3	cervix
27	chr22:31904400-31944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr22:31905000-31926400	Weak transcription	NHDF-Ad	bronchial
29	chr22:31905200-31957200	Weak transcription	A549	lung
30	chr22:31905600-31925600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr22:31905600-31926400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr22:31905600-31928800	Weak transcription	Aorta	Aorta
33	chr22:31905600-31946200	Weak transcription	Esophagus	oesophagus
34	chr22:31905800-31926400	Weak transcription	Osteobl	bone
35	chr22:31905800-31926600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr22:31905800-31926600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr22:31907400-31946400	Weak transcription	Brain Germinal Matrix	brain
38	chr22:31907400-31946600	Weak transcription	Left Ventricle	heart
39	chr22:31907600-31946200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr22:31907800-31934400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr22:31907800-31942800	Weak transcription	Fetal Intestine Large	intestine
42	chr22:31908000-31926400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr22:31908200-31925600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr22:31908200-31935200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr22:31910200-31934800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr22:31911600-31934600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr22:31911800-31934800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr22:31911800-31946000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr22:31912000-31926200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:31913800-31925200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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