Variant report

Variant	rs4848320
Chromosome Location	chr2:114010791-114010792
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	POLR2A	chr2:114010524-114011381	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114010394..114011259-chr2:114127840..114128840,2	MCF-7	breast:

Variant related genes	Relation type
PAX8-AS1	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1021409	0.81[AMR][1000 genomes]
rs12471722	0.87[AMR][1000 genomes]
rs1446246	0.83[JPT][hapmap]
rs2003986	0.81[AMR][1000 genomes]
rs2289897	0.81[AFR][1000 genomes]
rs4849186	0.81[AMR][1000 genomes]
rs745912	0.81[AMR][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4848320	LOC654433	cis	cerebellum	SCAN
rs4848320	LOC654433	cis	parietal	SCAN
rs4848320	AC016683.6	cis	Artery Tibial	GTEx
rs4848320	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs4848320	PAX8	cis	multi-tissue	Pritchard
rs4848320	PAX8	cis	lung	GTEx
rs4848320	AC016683.6	cis	Whole Blood	GTEx
rs4848320	AC016683.6	cis	lung	GTEx
rs4848320	PAX8	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:113999000-114014800	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:113999200-114013200	Weak transcription	Placenta	Placenta
4	chr2:113999600-114013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:113999600-114016400	Weak transcription	Fetal Stomach	stomach
6	chr2:113999600-114028400	Weak transcription	Ovary	ovary
7	chr2:114000200-114012000	Weak transcription	NHDF-Ad	bronchial
8	chr2:114000600-114011000	Weak transcription	Esophagus	oesophagus
9	chr2:114002400-114015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:114006600-114012200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:114006600-114016200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:114006600-114016200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:114006800-114015800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:114007200-114014800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:114007200-114016800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:114008000-114012000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr2:114008000-114013200	Weak transcription	HSMMtube	muscle
18	chr2:114008400-114011400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:114008400-114012600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:114008400-114012800	Enhancers	Fetal Thymus	thymus
21	chr2:114008400-114016000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:114008600-114012400	Weak transcription	A549	lung
23	chr2:114008800-114010800	Weak transcription	HSMM	muscle
24	chr2:114008800-114013200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:114009000-114013000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:114009000-114013000	Weak transcription	NH-A	brain
27	chr2:114009000-114013800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr2:114009000-114015000	Weak transcription	K562	blood
29	chr2:114009000-114015400	Weak transcription	Left Ventricle	heart
30	chr2:114009200-114014400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr2:114009200-114015400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:114009800-114011400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr2:114009800-114014000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:114009800-114019000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:114010000-114013000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:114010000-114016200	Enhancers	Primary T cells from cord blood	blood
37	chr2:114010000-114016200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr2:114010200-114010800	Enhancers	Thymus	Thymus
39	chr2:114010200-114011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:114010200-114012000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:114010200-114013000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:114010200-114013000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:114010200-114013000	Weak transcription	Lung	lung
44	chr2:114010200-114013800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:114010200-114014800	Weak transcription	Adipose Nuclei	Adipose
46	chr2:114010200-114014800	Weak transcription	Fetal Heart	heart
47	chr2:114010200-114014800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:114010200-114015000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:114010200-114015400	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr2:114010200-114015800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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