Variant report

Variant	rs6744286
Chromosome Location	chr2:114040823-114040824
allele	A/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	CTCF	chr2:114040700-114040850	GM12871	blood:	n/a	chr2:114040837-114040850 chr2:114040841-114040850
2	EP300	chr2:114040355-114042007	A549	lung:	n/a	chr2:114041601-114041617
3	REST	chr2:114040420-114040965	HepG2	liver:	n/a	chr2:114040737-114040750
4	POLR2A	chr2:114040475-114040852	A549	lung:	n/a	n/a
5	NFIC	chr2:114039914-114041352	HepG2	liver:	n/a	n/a
6	TCF12	chr2:114040512-114040987	A549	lung:	n/a	n/a
7	CTCF	chr2:114040720-114040870	AG04450	lung:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
8	CTCF	chr2:114040708-114040945	K562	blood:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
9	BHLHE40	chr2:114040418-114041081	HepG2	liver:	n/a	n/a
10	CTCF	chr2:114040760-114040910	HPAF	blood vessel:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
11	RAD21	chr2:114040553-114040990	HepG2	liver:	n/a	chr2:114040837-114040851 chr2:114040700-114040712 chr2:114040838-114040857 chr2:114040700-114040710
12	CTCF	chr2:114040700-114040850	SK-N-SH_RA	brain:	n/a	chr2:114040837-114040850 chr2:114040841-114040850
13	CTCF	chr2:114040769-114040897	A549	lung:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
14	YY1	chr2:114040615-114040888	K562	blood:	n/a	n/a
15	POLR2A	chr2:114040416-114040864	HepG2	liver:	n/a	n/a
16	CTCF	chr2:114040723-114040918	Gliobla	brain:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
17	EP300	chr2:114040470-114042086	ECC-1	luminal epithelium:	n/a	chr2:114042041-114042048 chr2:114041601-114041617
18	JUND	chr2:114040756-114040905	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr2:114040002-114042969	U87	brain:	n/a	n/a
20	GATA3	chr2:114040064-114041988	A549	lung:	n/a	chr2:114040943-114040953
21	RAD21	chr2:114040652-114041002	HepG2	liver:	n/a	chr2:114040837-114040851 chr2:114040700-114040712 chr2:114040838-114040857 chr2:114040700-114040710
22	MXI1	chr2:114040085-114041099	HepG2	liver:	n/a	chr2:114040778-114040787
23	CTCF	chr2:114040780-114040930	HAc	cerebellar:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
24	MBD4	chr2:114039913-114041064	HepG2	liver:	n/a	n/a
25	BRCA1	chr2:114040643-114040957	HepG2	liver:	n/a	n/a
26	MAX	chr2:114040664-114040921	K562	blood:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
27	HDAC2	chr2:114040028-114041071	HepG2	liver:	n/a	n/a
28	CTCF	chr2:114040800-114040950	HL-60	blood:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
29	CTCF	chr2:114040623-114041045	K562	blood:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
30	HDAC2	chr2:114040250-114041040	HepG2	liver:	n/a	n/a
31	SRF	chr2:114040457-114041013	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr2:114040467-114040858	HepG2	liver:	n/a	n/a
33	MAX	chr2:114039937-114040993	HepG2	liver:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040206-114040215 chr2:114040779-114040788
34	MAX	chr2:114040326-114041270	ECC-1	luminal epithelium:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
35	MAX	chr2:114040565-114041017	H1-hESC	embryonic stem cell:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
36	CEBPB	chr2:114040146-114040965	HepG2	liver:	n/a	n/a
37	CTCF	chr2:114040738-114040916	Lung_OC	lung:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
38	RAD21	chr2:114040627-114041093	A549	lung:	n/a	chr2:114040837-114040851 chr2:114040700-114040712 chr2:114040838-114040857 chr2:114040700-114040710
39	E2F6	chr2:114040365-114041180	A549	lung:	n/a	n/a
40	CTCF	chr2:114040760-114040910	GM06990	blood:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
41	FOXM1	chr2:114040291-114042129	ECC-1	luminal epithelium:	n/a	n/a
42	USF2	chr2:114040549-114040965	HepG2	liver:	n/a	n/a
43	CTCF	chr2:114040700-114040850	AG09309	skin:	n/a	chr2:114040837-114040850 chr2:114040841-114040850
44	ARID3A	chr2:114040264-114041172	HepG2	liver:	n/a	n/a
45	SIX5	chr2:114040598-114041732	A549	lung:	n/a	n/a
46	CTCF	chr2:114040740-114040890	HepG2	liver:	n/a	chr2:114040837-114040850 chr2:114040841-114040850 chr2:114040835-114040853 chr2:114040837-114040855 chr2:114040840-114040853
47	HEY1	chr2:114039910-114041181	HepG2	liver:	n/a	n/a
48	TBP	chr2:114040218-114041039	HepG2	liver:	n/a	n/a
49	MYC	chr2:114040416-114041801	MCF10A-Er-Src	breast:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040779-114040788
50	MAX	chr2:114039577-114042272	A549	lung:	n/a	chr2:114040779-114040788 chr2:114040778-114040788 chr2:114040779-114040788 chr2:114040777-114040785 chr2:114040778-114040789 chr2:114040206-114040215 chr2:114040779-114040788

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114040686..114041186-chr2:114127813..114128575,2	MCF-7	breast:
2	chr2:114033208..114035776-chr2:114039656..114042402,2	K562	blood:

Variant related genes	Relation type
PAX8	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1867763	0.80[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	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
2	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6744286	PAX8	cis	lung	GTEx
rs6744286	AC016683.6	cis	Esophagus Muscularis	GTEx
rs6744286	PAX8	cis	Nerve Tibial	GTEx
rs6744286	PAX8	cis	Esophagus Muscularis	GTEx
rs6744286	PAX8	cis	Whole Blood	GTEx
rs6744286	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs6744286	AC016683.6	cis	Esophagus Mucosa	GTEx
rs6744286	PAX8	cis	Esophagus Mucosa	GTEx
rs6744286	AC016683.6	cis	Whole Blood	GTEx
rs6744286	AC016683.6	cis	Nerve Tibial	GTEx
rs6744286	AC016683.6	cis	lung	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114036600-114043800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:114037400-114043600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:114037600-114042200	Enhancers	Pancreas	Pancrea
4	chr2:114037600-114043800	Enhancers	HMEC	breast
5	chr2:114038200-114043800	Enhancers	Fetal Intestine Large	intestine
6	chr2:114038400-114043600	Enhancers	Fetal Intestine Small	intestine
7	chr2:114038600-114043600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:114038600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:114039000-114041400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:114039000-114043800	Enhancers	HSMM	muscle
11	chr2:114039200-114041800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:114039400-114041800	Enhancers	NH-A	brain
13	chr2:114039400-114042000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:114039400-114043000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:114039400-114043200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:114039400-114043200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr2:114039600-114041400	Flanking Active TSS	A549	lung
18	chr2:114039600-114042200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:114039600-114042400	Enhancers	Adipose Nuclei	Adipose
20	chr2:114039600-114042600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:114039600-114043400	Enhancers	Osteobl	bone
22	chr2:114039600-114043600	Enhancers	HSMMtube	muscle
23	chr2:114039600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:114039800-114041200	Enhancers	Lung	lung
25	chr2:114039800-114041400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
26	chr2:114039800-114042200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr2:114039800-114042200	Enhancers	Stomach Mucosa	stomach
28	chr2:114039800-114043600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:114040000-114041000	Weak transcription	Brain Germinal Matrix	brain
30	chr2:114040000-114041000	Weak transcription	Small Intestine	intestine
31	chr2:114040000-114041200	Enhancers	Spleen	Spleen
32	chr2:114040000-114041600	Flanking Active TSS	HepG2	liver
33	chr2:114040000-114042200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr2:114040000-114042600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:114040200-114041400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:114040200-114041600	Enhancers	Colonic Mucosa	Colon
37	chr2:114040200-114041800	Enhancers	Right Ventricle	heart
38	chr2:114040200-114042600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr2:114040400-114041000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:114040400-114041200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:114040400-114041200	Weak transcription	Brain Anterior Caudate	brain
42	chr2:114040400-114041400	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:114040400-114042000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:114040400-114042000	Enhancers	Placenta	Placenta
45	chr2:114040400-114042200	Enhancers	Fetal Heart	heart
46	chr2:114040400-114042400	Enhancers	Fetal Muscle Leg	muscle
47	chr2:114040400-114042400	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr2:114040400-114042400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr2:114040400-114042800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr2:114040600-114041000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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