Variant report

Variant	rs5998054
Chromosome Location	chr22:31994406-31994407
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1044085	0.90[JPT][hapmap]
rs10775716	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12170867	0.90[JPT][hapmap]
rs12171042	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12627933	0.80[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs140078	0.82[MEX][hapmap]
rs140081	0.82[MEX][hapmap]
rs14034	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1543416	0.82[TSI][hapmap]
rs2024747	0.85[JPT][hapmap]
rs2092905	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236033	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2281440	0.85[ASN][1000 genomes]
rs2295242	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2295251	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[ASN][1000 genomes]
rs2387	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3804087	0.83[MEX][hapmap]
rs3818134	0.82[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap]
rs4820051	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4820979	0.82[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap]
rs4820980	0.85[JPT][hapmap];0.89[MEX][hapmap]
rs4820983	0.82[TSI][hapmap]
rs5749293	0.85[JPT][hapmap]
rs5749303	0.90[JPT][hapmap]
rs5749304	0.95[CEU][hapmap];0.82[JPT][hapmap]
rs5749306	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs5753667	0.82[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs5753681	0.85[JPT][hapmap]
rs5753686	0.82[TSI][hapmap]
rs5753690	0.84[EUR][1000 genomes]
rs5753691	0.95[CEU][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs5753713	0.86[ASN][1000 genomes]
rs5753714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753715	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs5753716	0.80[ASN][1000 genomes]
rs5753732	0.85[ASN][1000 genomes]
rs5753733	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5753734	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5994415	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998042	0.82[TSI][hapmap]
rs5998086	0.83[MEX][hapmap]
rs7289075	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7291918	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs738656	0.82[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap]
rs738684	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs738702	0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs761746	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[ASN][1000 genomes]
rs761747	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8461	0.83[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs9956	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914980	chr22:31966274-32024980	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv517534	chr22:31977594-32024980	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5998054	HORMAD2	cis	parietal	SCAN
rs5998054	SFI1	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31935800-32013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr22:31947800-32009600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr22:31949400-32014400	Weak transcription	Hela-S3	cervix
4	chr22:31957400-32016400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:31968800-32003800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr22:31974400-31998200	Weak transcription	Small Intestine	intestine
7	chr22:31974800-31998200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr22:31975000-32003800	Weak transcription	Aorta	Aorta
9	chr22:31976200-32014800	Weak transcription	A549	lung
10	chr22:31976400-32014800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr22:31976400-32019200	Weak transcription	Fetal Brain Male	brain
12	chr22:31981800-31995600	Weak transcription	HUVEC	blood vessel
13	chr22:31982000-31998000	Weak transcription	Brain Angular Gyrus	brain
14	chr22:31982400-31998200	Weak transcription	Gastric	stomach
15	chr22:31982600-31997400	Weak transcription	Brain Hippocampus Middle	brain
16	chr22:31982600-31998000	Weak transcription	NHEK	skin
17	chr22:31982600-31998400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr22:31982600-32006400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr22:31982800-31997600	Weak transcription	Colon Smooth Muscle	Colon
20	chr22:31982800-31998200	Weak transcription	NHLF	lung
21	chr22:31983000-31998600	Weak transcription	Colonic Mucosa	Colon
22	chr22:31983600-31998000	Weak transcription	Spleen	Spleen
23	chr22:31983800-31996400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr22:31984400-31996400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr22:31984400-31996800	Weak transcription	GM12878-XiMat	blood
26	chr22:31984400-31998000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr22:31984400-31998000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr22:31984400-31998200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr22:31984400-31998400	Weak transcription	Primary B cells from cord blood	blood
30	chr22:31984400-31998400	Weak transcription	Adipose Nuclei	Adipose
31	chr22:31984400-31998400	Weak transcription	Fetal Lung	lung
32	chr22:31984400-31999000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr22:31984600-31996200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr22:31984600-31997600	Weak transcription	Fetal Muscle Leg	muscle
35	chr22:31984600-31997800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr22:31984600-31998000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr22:31984600-31998200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr22:31984600-31998200	Weak transcription	Ovary	ovary
39	chr22:31985200-31998200	Weak transcription	Fetal Brain Female	brain
40	chr22:31985600-31997800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr22:31985600-31998000	Weak transcription	Osteobl	bone
42	chr22:31985600-31998400	Weak transcription	Brain Anterior Caudate	brain
43	chr22:31985600-32014000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr22:31985800-31996000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr22:31985800-31996000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr22:31985800-31996400	Weak transcription	Dnd41	blood
47	chr22:31985800-31996600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr22:31985800-31996600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr22:31985800-31996600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr22:31985800-31996800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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