Variant report

Variant	rs11886472
Chromosome Location	chr2:114003237-114003238
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	MAFK	chr2:114003013-114003416	HepG2	liver:	n/a	chr2:114003236-114003247 chr2:114003232-114003248 chr2:114003237-114003248 chr2:114003228-114003245 chr2:114003232-114003247
2	MYBL2	chr2:114002719-114003341	HepG2	liver:	n/a	n/a
3	HNF4G	chr2:114002797-114003247	HepG2	liver:	n/a	chr2:114002996-114003011 chr2:114002997-114003010
4	HNF4G	chr2:114002799-114003338	HepG2	liver:	n/a	chr2:114002996-114003011 chr2:114002997-114003010
5	HNF4A	chr2:114002816-114003596	HepG2	liver:	n/a	chr2:114002997-114003010
6	POLR2A	chr2:114002793-114003697	ECC-1	luminal epithelium:	n/a	n/a
7	SP1	chr2:114002835-114003325	HepG2	liver:	n/a	n/a
8	HNF4A	chr2:114002806-114003260	HepG2	liver:	n/a	chr2:114002997-114003010
9	HNF4A	chr2:114002814-114003250	HepG2	liver:	n/a	chr2:114002997-114003010
10	POLR2A	chr2:114002827-114003264	ECC-1	luminal epithelium:	n/a	n/a
11	MYBL2	chr2:114002819-114003352	HepG2	liver:	n/a	n/a
12	MAZ	chr2:114003092-114003279	HepG2	liver:	n/a	n/a
13	MAFK	chr2:114003055-114003625	HepG2	liver:	n/a	chr2:114003236-114003247 chr2:114003232-114003248 chr2:114003237-114003248 chr2:114003228-114003245 chr2:114003232-114003247
14	MAFF	chr2:114003044-114003380	HepG2	liver:	n/a	chr2:114003231-114003249
15	HDAC2	chr2:114002808-114003239	HepG2	liver:	n/a	n/a
16	SMC3	chr2:114002914-114003345	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:114000599..114003472-chr2:114003637..114006808,6	K562	blood:
2	chr2:113992095..113996138-chr2:114002471..114005425,4	MCF-7	breast:
3	chr2:113997900..114001469-chr2:114001503..114004857,6	MCF-7	breast:
4	chr2:114000063..114003907-chr2:114004909..114007665,4	MCF-7	breast:
5	chr2:113960427..113963298-chr2:114003216..114006590,3	MCF-7	breast:

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000189223	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000258395	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11884791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11886592	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11903972	0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs13015478	0.86[YRI][hapmap]
rs13396369	1.00[JPT][hapmap]
rs1374163	1.00[JPT][hapmap]
rs17043146	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17043176	0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2018348	0.86[YRI][hapmap]
rs3762498	0.87[AFR][1000 genomes]
rs73955185	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73955186	0.81[AMR][1000 genomes];0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11886472	PAX8	cis	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
7	chr2:113998200-114006600	Weak transcription	Fetal Thymus	thymus
8	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:113999000-114014800	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:113999200-114005200	Weak transcription	Gastric	stomach
11	chr2:113999200-114007000	Weak transcription	Right Atrium	heart
12	chr2:113999200-114009400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:113999200-114013200	Weak transcription	Placenta	Placenta
14	chr2:113999400-114006600	Weak transcription	Colonic Mucosa	Colon
15	chr2:113999400-114009400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:113999600-114006600	Weak transcription	K562	blood
17	chr2:113999600-114007000	Weak transcription	HSMMtube	muscle
18	chr2:113999600-114013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:113999600-114016400	Weak transcription	Fetal Stomach	stomach
20	chr2:113999600-114028400	Weak transcription	Ovary	ovary
21	chr2:113999800-114005200	Weak transcription	Lung	lung
22	chr2:113999800-114006800	Weak transcription	NHLF	lung
23	chr2:114000000-114006600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:114000000-114007000	Weak transcription	HSMM	muscle
25	chr2:114000200-114006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:114000200-114009200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:114000200-114012000	Weak transcription	NHDF-Ad	bronchial
28	chr2:114000600-114006600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:114000600-114011000	Weak transcription	Esophagus	oesophagus
30	chr2:114001000-114003600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:114001000-114004000	Enhancers	Fetal Intestine Large	intestine
32	chr2:114001200-114003600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr2:114001400-114003600	Enhancers	A549	lung
34	chr2:114001600-114003600	Enhancers	Adipose Nuclei	Adipose
35	chr2:114001600-114003800	Enhancers	Fetal Intestine Small	intestine
36	chr2:114001600-114004800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:114001800-114003600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:114001800-114003800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:114001800-114003800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr2:114002000-114003600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:114002000-114004200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:114002000-114006800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:114002000-114006800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:114002200-114004000	Enhancers	Liver	Liver
45	chr2:114002400-114015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:114003000-114003600	Enhancers	Fetal Lung	lung
47	chr2:114003000-114003800	Enhancers	Fetal Muscle Leg	muscle
48	chr2:114003000-114004800	Enhancers	NHEK	skin
49	chr2:114003200-114003400	Enhancers	HepG2	liver
50	chr2:114003200-114003600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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