Variant report

Variant	rs2863244
Chromosome Location	chr2:114000866-114000867
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	POLR2A	chr2:113998335-114000919	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:113996944-114000866	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:114000426..114002029-chr2:114005255..114006770,2	MCF-7	breast:
2	chr2:114000599..114003472-chr2:114003637..114006808,6	K562	blood:
3	chr2:113954862..113956783-chr2:113998620..114001129,2	MCF-7	breast:
4	chr2:114000063..114003907-chr2:114004909..114007665,4	MCF-7	breast:

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11123173	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12990456	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13429413	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374161	0.81[JPT][hapmap]
rs1374163	0.82[YRI][hapmap]
rs1466018	0.87[JPT][hapmap]
rs1491584	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1491585	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1491586	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs35129549	0.83[ASN][1000 genomes]
rs4142815	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4849187	0.87[ASN][1000 genomes]
rs6542127	0.87[JPT][hapmap]
rs6726151	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6734610	0.94[ASW][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560701	0.87[JPT][hapmap]

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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2863244	AC016683.6	cis	lung	GTEx
rs2863244	PAX8	cis	Skin Sun Exposed Lower leg	GTEx
rs2863244	PAX8	cis	parietal	SCAN
rs2863244	LOC654433	cis	cerebellum	SCAN
rs2863244	AC016683.6	cis	Whole Blood	GTEx
rs2863244	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs2863244	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs2863244	PAX8	cis	lymphoblastoid	seeQTL
rs2863244	LOC654433	cis	parietal	SCAN
rs2863244	AC016683.6	cis	Artery Tibial	GTEx
rs2863244	AC016683.6	cis	Esophagus Mucosa	GTEx
rs2863244	AC016683.6	cis	Esophagus Muscularis	GTEx
rs2863244	AC016683.6	cis	Muscle Skeletal	GTEx
rs2863244	RP11-65I12.1	cis	Esophagus Mucosa	GTEx
rs2863244	PAX8	cis	Esophagus Mucosa	GTEx
rs2863244	AC016683.6	cis	Thyroid	GTEx
rs2863244	PAX8	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:55 , 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	chr2:113994200-114002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
8	chr2:113997600-114001000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr2:113998200-114006600	Weak transcription	Fetal Thymus	thymus
10	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:113998800-114001400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:113998800-114001600	Weak transcription	Fetal Intestine Small	intestine
13	chr2:113998800-114002200	Weak transcription	Liver	Liver
14	chr2:113999000-114001400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:113999000-114001600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:113999000-114001800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:113999000-114003000	Weak transcription	Fetal Lung	lung
18	chr2:113999000-114014800	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:113999200-114005200	Weak transcription	Gastric	stomach
20	chr2:113999200-114007000	Weak transcription	Right Atrium	heart
21	chr2:113999200-114009400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:113999200-114013200	Weak transcription	Placenta	Placenta
23	chr2:113999400-114006600	Weak transcription	Colonic Mucosa	Colon
24	chr2:113999400-114009400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:113999600-114003200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:113999600-114006600	Weak transcription	K562	blood
27	chr2:113999600-114007000	Weak transcription	HSMMtube	muscle
28	chr2:113999600-114013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:113999600-114016400	Weak transcription	Fetal Stomach	stomach
30	chr2:113999600-114028400	Weak transcription	Ovary	ovary
31	chr2:113999800-114001000	Weak transcription	Fetal Intestine Large	intestine
32	chr2:113999800-114002000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:113999800-114005200	Weak transcription	Lung	lung
34	chr2:113999800-114006800	Weak transcription	NHLF	lung
35	chr2:114000000-114001200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:114000000-114001600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:114000000-114001800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:114000000-114003000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:114000000-114006600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:114000000-114007000	Weak transcription	HSMM	muscle
41	chr2:114000200-114001400	Weak transcription	A549	lung
42	chr2:114000200-114001600	Weak transcription	Adipose Nuclei	Adipose
43	chr2:114000200-114003000	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:114000200-114003000	Weak transcription	NHEK	skin
45	chr2:114000200-114006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:114000200-114009200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:114000200-114012000	Weak transcription	NHDF-Ad	bronchial
48	chr2:114000400-114002000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:114000600-114002600	Strong transcription	Fetal Kidney	kidney
50	chr2:114000600-114006600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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