Variant report

Variant	rs4820962
Chromosome Location	chr22:31689951-31689952
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr22:31689660-31689952	K562	blood:	n/a	chr22:31689759-31689772
2	MEF2A	chr22:31689698-31689992	GM12878	blood:	n/a	chr22:31689858-31689873 chr22:31689859-31689873
3	POLR2A	chr22:31689705-31690237	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr22:31689621-31690006	MCF10A-Er-Src	breast:	n/a	chr22:31689844-31689855 chr22:31689846-31689854
5	MEF2A	chr22:31689634-31690081	K562	blood:	n/a	chr22:31689858-31689873 chr22:31689859-31689873
6	FOS	chr22:31689700-31689952	HUVEC	blood vessel:	n/a	chr22:31689844-31689855 chr22:31689846-31689854
7	SETDB1	chr22:31689774-31690080	U2OS	brain:	n/a	n/a
8	POLR2A	chr22:31689555-31689966	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr22:31689699-31689993	K562	blood:	n/a	chr22:31689846-31689854
10	MEF2A	chr22:31689623-31690073	SK-N-SH	brain:	n/a	chr22:31689858-31689873 chr22:31689859-31689873
11	CEBPB	chr22:31689717-31689987	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31685822..31687584-chr22:31689344..31691234,2	K562	blood:
2	chr22:31683915..31694680-chr22:31733392..31744713,34	MCF-7	breast:
3	chr22:31684664..31691252-chr22:31735490..31744100,29	MCF-7	breast:

Variant related genes	Relation type
PIK3IP1	TF binding region
ENSG00000100100	Chromatin interaction
ENSG00000100105	Chromatin interaction
ENSG00000213888	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1034588	0.86[EUR][1000 genomes]
rs1034589	0.81[EUR][1000 genomes]
rs12152166	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13054220	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131205	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1858821	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2040533	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2073857	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2078803	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2079431	0.81[EUR][1000 genomes]
rs2106294	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2228619	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283879	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2283881	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2413033	0.81[EUR][1000 genomes]
rs2413034	0.82[EUR][1000 genomes]
rs2413035	0.85[EUR][1000 genomes]
rs2413046	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2413047	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2413049	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4141404	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4299418	0.85[EUR][1000 genomes]
rs4603880	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4820042	0.85[EUR][1000 genomes]
rs4820043	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4820951	0.85[EUR][1000 genomes]
rs4820963	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5749224	0.81[EUR][1000 genomes]
rs5749229	0.85[EUR][1000 genomes]
rs5749243	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5753500	0.81[EUR][1000 genomes]
rs5753521	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753543	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997902	0.83[EUR][1000 genomes]
rs5997912	0.85[EUR][1000 genomes]
rs5997913	0.82[EUR][1000 genomes]
rs5997933	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5997939	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997949	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71324184	0.84[EUR][1000 genomes]
rs714909	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs715510	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7287267	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737684	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs737887	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737888	0.86[EUR][1000 genomes]
rs8135344	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8135347	0.82[EUR][1000 genomes]
rs8138596	0.84[EUR][1000 genomes]
rs9606830	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9606831	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609254	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609257	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609264	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609265	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609266	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609267	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9609268	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9621235	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4820962	SFI1	cis	Thyroid	GTEx
rs4820962	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31686600-31690400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr22:31688400-31693400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:31688600-31690000	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr22:31688600-31690000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
5	chr22:31688600-31690000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr22:31688600-31690000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr22:31688600-31690000	Enhancers	Fetal Heart	heart
8	chr22:31688600-31690000	Enhancers	Fetal Intestine Large	intestine
9	chr22:31688600-31690000	Enhancers	Stomach Mucosa	stomach
10	chr22:31688600-31690000	Enhancers	HUVEC	blood vessel
11	chr22:31688600-31690600	Weak transcription	Small Intestine	intestine
12	chr22:31688600-31691200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr22:31688600-31691400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr22:31688600-31691800	Weak transcription	Left Ventricle	heart
15	chr22:31688800-31690000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr22:31688800-31690000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr22:31688800-31690000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr22:31688800-31690000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr22:31688800-31690000	Enhancers	Hela-S3	cervix
20	chr22:31688800-31690000	Enhancers	NHLF	lung
21	chr22:31688800-31690200	Enhancers	Primary B cells from peripheral blood	blood
22	chr22:31688800-31690200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr22:31688800-31690200	Enhancers	Fetal Thymus	thymus
24	chr22:31688800-31690800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr22:31688800-31691400	Weak transcription	A549	lung
26	chr22:31688800-31691400	Weak transcription	HMEC	breast
27	chr22:31688800-31691600	Weak transcription	Psoas Muscle	Psoas
28	chr22:31688800-31692000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr22:31688800-31692000	Weak transcription	Colonic Mucosa	Colon
30	chr22:31688800-31692400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:31688800-31692400	Weak transcription	Fetal Lung	lung
32	chr22:31688800-31693000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr22:31689000-31690000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr22:31689000-31690000	Enhancers	Brain Hippocampus Middle	brain
35	chr22:31689000-31690000	Enhancers	Colon Smooth Muscle	Colon
36	chr22:31689000-31690200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr22:31689000-31691400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr22:31689000-31691400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr22:31689000-31691600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr22:31689000-31691600	Enhancers	GM12878-XiMat	blood
41	chr22:31689000-31691800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr22:31689000-31696400	Weak transcription	HepG2	liver
43	chr22:31689200-31690000	Enhancers	Duodenum Mucosa	Duodenum
44	chr22:31689200-31690000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr22:31689200-31690000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr22:31689200-31690600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr22:31689200-31690600	Enhancers	Stomach Smooth Muscle	stomach
48	chr22:31689200-31690800	Enhancers	Rectal Smooth Muscle	rectum
49	chr22:31689200-31691400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr22:31689200-31691400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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