Variant report

Variant	rs9606852
Chromosome Location	chr22:31910355-31910356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13057504	0.80[AMR][1000 genomes]
rs2273251	0.81[AMR][1000 genomes]
rs34538851	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5749283	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5749286	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5749291	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749298	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753615	0.80[AMR][1000 genomes]
rs5753621	0.82[AMR][1000 genomes]
rs5753628	0.82[AMR][1000 genomes]
rs5753631	0.84[AMR][1000 genomes]
rs5753648	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753659	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753661	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753664	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753665	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753666	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753669	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753671	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7284622	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7285619	0.82[AMR][1000 genomes]
rs8139625	0.80[AMR][1000 genomes]
rs8142121	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9606843	0.83[AMR][1000 genomes]
rs9606846	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9606847	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9606848	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609286	0.81[AMR][1000 genomes]
rs9609295	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609296	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9609297	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609299	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609301	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609303	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609304	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9606852	SFI1	cis	Thyroid	GTEx
rs9606852	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31893200-31912200	Weak transcription	Small Intestine	intestine
2	chr22:31893200-31934800	Weak transcription	Ovary	ovary
3	chr22:31893400-31920400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:31893400-31971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr22:31893600-31925600	Weak transcription	Gastric	stomach
6	chr22:31893600-31926200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr22:31893600-31928200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr22:31893600-31934800	Weak transcription	Pancreas	Pancrea
9	chr22:31893600-31946600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr22:31893600-31970000	Weak transcription	Colonic Mucosa	Colon
11	chr22:31893800-31913400	Weak transcription	Fetal Muscle Leg	muscle
12	chr22:31893800-31914600	Weak transcription	HepG2	liver
13	chr22:31893800-31921800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr22:31893800-31924600	Weak transcription	Adipose Nuclei	Adipose
15	chr22:31893800-31924600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr22:31893800-31925200	Weak transcription	Brain Hippocampus Middle	brain
17	chr22:31893800-31925400	Weak transcription	Brain Angular Gyrus	brain
18	chr22:31893800-31925600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr22:31893800-31926400	Weak transcription	Fetal Lung	lung
20	chr22:31893800-31927000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr22:31893800-31934800	Weak transcription	HMEC	breast
22	chr22:31893800-31945600	Weak transcription	Brain Anterior Caudate	brain
23	chr22:31894000-31913200	Weak transcription	K562	blood
24	chr22:31894000-31926400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr22:31894000-31946600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr22:31894000-31946600	Weak transcription	Fetal Brain Female	brain
27	chr22:31894400-31913600	Weak transcription	Primary B cells from cord blood	blood
28	chr22:31895400-31931200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:31897200-31924800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr22:31898000-31934800	Weak transcription	Spleen	Spleen
31	chr22:31900200-31914600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr22:31900200-31926400	Weak transcription	HSMM	muscle
33	chr22:31900600-31913600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr22:31900800-31919000	Weak transcription	HUVEC	blood vessel
35	chr22:31900800-31940800	Weak transcription	NHEK	skin
36	chr22:31901000-31911000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr22:31901000-31926200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr22:31901000-31926400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr22:31901800-31926000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr22:31902000-31914000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr22:31902400-31915000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr22:31903400-31934400	Weak transcription	Hela-S3	cervix
43	chr22:31903600-31913800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr22:31903800-31910600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr22:31903800-31913600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr22:31904400-31944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr22:31904600-31912000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr22:31904600-31914200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr22:31904600-31918600	Strong transcription	Primary T cells from cord blood	blood
50	chr22:31904800-31912200	Strong transcription	Fetal Thymus	thymus

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