Variant report

Variant	rs10193733
Chromosome Location	chr2:113992624-113992625
allele	C/T
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	EP300	chr2:113992390-113992628	K562	blood:	n/a	n/a
2	MYC	chr2:113992469-113993469	K562	blood:	n/a	n/a
3	MAX	chr2:113992430-113993533	HCT-116	colon:	n/a	n/a
4	MAX	chr2:113992607-113993492	K562	blood:	n/a	n/a
5	TEAD4	chr2:113992284-113992742	K562	blood:	n/a	n/a
6	IRF1	chr2:113992533-113993274	K562	blood:	n/a	n/a
7	POLR2A	chr2:113992566-113993492	ECC-1	luminal epithelium:	n/a	n/a
8	JUND	chr2:113992426-113993291	K562	blood:	n/a	n/a
9	MYC	chr2:113992518-113993471	K562	blood:	n/a	n/a
10	GATA2	chr2:113992284-113992725	K562	blood:	n/a	chr2:113992652-113992663
11	POLR2A	chr2:113992474-113993420	HCT-116	colon:	n/a	n/a
12	E2F6	chr2:113992478-113993456	K562	blood:	n/a	chr2:113992603-113992620 chr2:113993249-113993258 chr2:113992626-113992640
13	POLR2A	chr2:113992610-113993624	SK-N-MC	brain:	n/a	n/a
14	TAL1	chr2:113992338-113992674	K562	blood:	n/a	n/a
15	RCOR1	chr2:113992366-113993293	K562	blood:	n/a	n/a
16	NR2F2	chr2:113992211-113993570	K562	blood:	n/a	n/a
17	MAZ	chr2:113992543-113993334	K562	blood:	n/a	n/a
18	TEAD4	chr2:113992350-113992644	K562	blood:	n/a	n/a
19	GATA1	chr2:113992509-113993207	PBDE	blood:	n/a	chr2:113992652-113992663
20	NR2F2	chr2:113992327-113992788	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113968914..113973967-chr2:113991743..113995400,6	MCF-7	breast:
2	chr2:113968482..113971643-chr2:113991034..113994286,5	MCF-7	breast:
3	chr2:113973621..113980487-chr2:113991287..113996231,8	K562	blood:

Variant related genes	Relation type
PAX8-AS1	TF binding region
ENSG00000189223	Chromatin interaction
ENSG00000125618	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3748915	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762498	0.82[AFR][1000 genomes]
rs56865224	0.81[AFR][1000 genomes]
rs6707386	0.81[AFR][1000 genomes]
rs7572615	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10193733	PAX8	cis	Nerve Tibial	GTEx
rs10193733	AC016683.6	cis	Whole Blood	GTEx
rs10193733	AC016683.6	cis	Muscle Skeletal	GTEx
rs10193733	PAX8	cis	Esophagus Mucosa	GTEx
rs10193733	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs10193733	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs10193733	AC016683.6	cis	Nerve Tibial	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113984000-113998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:113987000-113997000	Weak transcription	Hela-S3	cervix
3	chr2:113987800-113992800	Weak transcription	Fetal Kidney	kidney
4	chr2:113991400-113993000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:113991400-113993000	Enhancers	NHDF-Ad	bronchial
6	chr2:113991400-113993000	Enhancers	NHLF	lung
7	chr2:113991400-113993200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:113991800-113992800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:113991800-113997000	Weak transcription	Spleen	Spleen
10	chr2:113992000-113994800	Weak transcription	HepG2	liver
11	chr2:113992000-113997000	Weak transcription	Esophagus	oesophagus
12	chr2:113992000-113997000	Weak transcription	Fetal Heart	heart
13	chr2:113992000-113997000	Weak transcription	Right Atrium	heart
14	chr2:113992000-113997400	Weak transcription	Left Ventricle	heart
15	chr2:113992000-113997400	Weak transcription	Right Ventricle	heart
16	chr2:113992200-113992800	Weak transcription	NHEK	skin
17	chr2:113992200-113993200	Enhancers	A549	lung
18	chr2:113992400-113992800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:113992400-113992800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr2:113992400-113992800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:113992400-113992800	Enhancers	Placenta	Placenta
22	chr2:113992400-113992800	Flanking Active TSS	Dnd41	blood
23	chr2:113992400-113992800	Flanking Active TSS	K562	blood
24	chr2:113992400-113993000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr2:113992400-113993400	Active TSS	GM12878-XiMat	blood
26	chr2:113992600-113992800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:113992600-113992800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:113992600-113992800	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr2:113992600-113992800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr2:113992600-113992800	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr2:113992600-113992800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr2:113992600-113992800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:113992600-113992800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:113992600-113992800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:113992600-113992800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:113992600-113992800	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr2:113992600-113992800	Enhancers	Lung	lung
38	chr2:113992600-113993000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
39	chr2:113992600-113993000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:113992600-113993000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:113992600-113993000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr2:113992600-113993000	Flanking Active TSS	Fetal Muscle Trunk	muscle
43	chr2:113992600-113993000	Enhancers	Stomach Mucosa	stomach
44	chr2:113992600-113993400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:113992600-113993400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:113992600-113993400	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr2:113992600-113993400	Active TSS	Liver	Liver
48	chr2:113992600-113993400	ZNF genes & repeats	Fetal Thymus	thymus
49	chr2:113992600-113993400	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr2:113992600-113993400	Active TSS	Monocytes-CD14+_RO01746	blood

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