Variant report

Variant	rs12999288
Chromosome Location	chr2:114040144-114040145
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	NFIC	chr2:114039914-114041352	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:114039789-114040167	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr2:114040002-114042969	U87	brain:	n/a	n/a
4	GATA3	chr2:114040064-114041988	A549	lung:	n/a	chr2:114040943-114040953
5	MXI1	chr2:114040085-114041099	HepG2	liver:	n/a	chr2:114040778-114040787
6	MBD4	chr2:114039913-114041064	HepG2	liver:	n/a	n/a
7	HDAC2	chr2:114040028-114041071	HepG2	liver:	n/a	n/a
8	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
9	HEY1	chr2:114039910-114041181	HepG2	liver:	n/a	n/a
10	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
11	SP1	chr2:114039766-114041029	HepG2	liver:	n/a	chr2:114040737-114040751 chr2:114039879-114039889
12	POLR2A	chr2:114039944-114040383	ECC-1	luminal epithelium:	n/a	n/a
13	MBD4	chr2:114039903-114041274	HepG2	liver:	n/a	n/a
14	MAX	chr2:114039802-114041133	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
15	HEY1	chr2:114039897-114041122	HepG2	liver:	n/a	n/a
16	TEAD4	chr2:114040143-114041304	HepG2	liver:	n/a	n/a
17	HNF4A	chr2:114039804-114040975	HepG2	liver:	n/a	chr2:114040449-114040461 chr2:114040448-114040462 chr2:114040448-114040463 chr2:114040448-114040461
18	POLR2A	chr2:114039944-114042862	U87	brain:	n/a	n/a
19	POLR2A	chr2:114039871-114041120	HepG2	liver:	n/a	n/a
20	MAX	chr2:114039600-114041719	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
21	POLR2A	chr2:114039941-114040975	HepG2	liver:	n/a	n/a
22	SP1	chr2:114040009-114042296	A549	lung:	n/a	chr2:114040737-114040751
23	POLR2A	chr2:114039883-114041078	HepG2	liver:	n/a	n/a
24	ZBTB7A	chr2:114039895-114040361	HepG2	liver:	n/a	n/a
25	RXRA	chr2:114039976-114041006	HepG2	liver:	n/a	chr2:114039998-114040005 chr2:114039991-114040004 chr2:114039991-114040004 chr2:114039987-114040007 chr2:114040833-114040853
26	NFIC	chr2:114039857-114041153	HepG2	liver:	n/a	n/a
27	MYBL2	chr2:114039554-114041115	HepG2	liver:	n/a	n/a
28	REST	chr2:114040036-114041988	A549	lung:	n/a	chr2:114041552-114041565 chr2:114041825-114041838 chr2:114040737-114040750 chr2:114041823-114041833
29	POLR2A	chr2:114039989-114041053	HepG2	liver:	n/a	n/a
30	TCF12	chr2:114039879-114042422	A549	lung:	n/a	chr2:114039947-114039956 chr2:114041607-114041617
31	ZBTB7A	chr2:114039979-114041225	ECC-1	luminal epithelium:	n/a	n/a
32	FOXA1	chr2:114039742-114041036	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:114039876-114041153	HepG2	liver:	n/a	n/a
34	MYBL2	chr2:114039715-114041218	HepG2	liver:	n/a	n/a
35	YY1	chr2:114039898-114040245	HepG2	liver:	n/a	n/a
36	POLR2A	chr2:114040005-114040378	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114033208..114035776-chr2:114039656..114042402,2	K562	blood:

Variant related genes	Relation type
PAX8	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10864913	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11685107	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11685421	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11691437	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11695071	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12476331	0.88[ASN][1000 genomes]
rs12478795	0.88[ASN][1000 genomes]
rs13015130	0.88[ASN][1000 genomes]
rs1900216	0.88[ASN][1000 genomes]
rs35006857	0.88[ASN][1000 genomes]
rs4848321	0.88[ASN][1000 genomes]
rs6716573	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7425070	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs877202	0.88[ASN][1000 genomes]
rs895416	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs895417	0.88[ASN][1000 genomes]
rs935365	0.88[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	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12999288	AC016683.6	cis	lung	GTEx
rs12999288	AC016683.6	cis	Esophagus Muscularis	GTEx
rs12999288	PAX8	cis	Esophagus Muscularis	GTEx
rs12999288	PAX8	cis	Whole Blood	GTEx
rs12999288	AC016683.6	cis	Whole Blood	GTEx
rs12999288	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs12999288	PAX8	cis	lung	GTEx
rs12999288	AC016683.6	cis	Artery Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114036600-114043800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:114037400-114040600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:114037400-114043600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:114037600-114042200	Enhancers	Pancreas	Pancrea
5	chr2:114037600-114043800	Enhancers	HMEC	breast
6	chr2:114038200-114043800	Enhancers	Fetal Intestine Large	intestine
7	chr2:114038400-114043600	Enhancers	Fetal Intestine Small	intestine
8	chr2:114038600-114040800	Enhancers	NHEK	skin
9	chr2:114038600-114043600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:114038600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:114039000-114040600	Weak transcription	NHDF-Ad	bronchial
12	chr2:114039000-114041400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:114039000-114043800	Enhancers	HSMM	muscle
14	chr2:114039200-114041800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:114039400-114040400	Enhancers	Duodenum Mucosa	Duodenum
16	chr2:114039400-114041800	Enhancers	NH-A	brain
17	chr2:114039400-114042000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:114039400-114043000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:114039400-114043200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:114039400-114043200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr2:114039600-114040400	Enhancers	Brain Hippocampus Middle	brain
22	chr2:114039600-114041400	Flanking Active TSS	A549	lung
23	chr2:114039600-114042200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:114039600-114042400	Enhancers	Adipose Nuclei	Adipose
25	chr2:114039600-114042600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:114039600-114043400	Enhancers	Osteobl	bone
27	chr2:114039600-114043600	Enhancers	HSMMtube	muscle
28	chr2:114039600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:114039800-114040200	Bivalent Enhancer	Fetal Kidney	kidney
30	chr2:114039800-114040400	Bivalent Enhancer	Fetal Muscle Leg	muscle
31	chr2:114039800-114040600	Enhancers	Gastric	stomach
32	chr2:114039800-114041200	Enhancers	Lung	lung
33	chr2:114039800-114041400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
34	chr2:114039800-114042200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr2:114039800-114042200	Enhancers	Stomach Mucosa	stomach
36	chr2:114039800-114043600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:114040000-114040200	Enhancers	Brain Anterior Caudate	brain
38	chr2:114040000-114040200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:114040000-114040200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
40	chr2:114040000-114040600	Flanking Active TSS	Liver	Liver
41	chr2:114040000-114040800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr2:114040000-114041000	Weak transcription	Brain Germinal Matrix	brain
43	chr2:114040000-114041000	Weak transcription	Small Intestine	intestine
44	chr2:114040000-114041200	Enhancers	Spleen	Spleen
45	chr2:114040000-114041600	Flanking Active TSS	HepG2	liver
46	chr2:114040000-114042200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr2:114040000-114042600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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