Variant report

Variant	rs35920363
Chromosome Location	chr2:113996339-113996340
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	chr2:113996308-113996594	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113955248..113957880-chr2:113994557..113996875,2	MCF-7	breast:
2	chr2:113958931..113961853-chr2:113995609..113998129,2	K562	blood:
3	chr2:113970934..113973261-chr2:113995727..113997421,2	MCF-7	breast:

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000258395	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1139015	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13015478	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2018348	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs35129549	0.80[AMR][1000 genomes]
rs3762497	0.84[AFR][1000 genomes];0.88[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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs35920363	PAX8	cis	Adipose Subcutaneous	GTEx
rs35920363	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs35920363	AC016683.6	cis	Heart Left Ventricle	GTEx
rs35920363	AC016683.6	cis	Skin Sun Exposed Lower leg	GTEx
rs35920363	AC016683.6	cis	lung	GTEx
rs35920363	PAX8	cis	lung	GTEx
rs35920363	AC016683.6	cis	Esophagus Mucosa	GTEx
rs35920363	AC016683.6	cis	Whole Blood	GTEx
rs35920363	PAX8	cis	Whole Blood	GTEx
rs35920363	AC016683.6	cis	Artery Tibial	GTEx
rs35920363	AC016683.6	cis	Esophagus Muscularis	GTEx
rs35920363	PAX8	cis	Esophagus Mucosa	GTEx
rs35920363	PAX8	cis	Esophagus Muscularis	GTEx
rs35920363	PAX8	cis	Artery Tibial	GTEx
rs35920363	AC016683.6	cis	Nerve Tibial	GTEx
rs35920363	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs35920363	AC016683.6	cis	Muscle Skeletal	GTEx
rs35920363	PAX8	cis	Nerve Tibial	GTEx
rs35920363	PAX8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113984000-113998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:113987000-113997000	Weak transcription	Hela-S3	cervix
3	chr2:113991800-113997000	Weak transcription	Spleen	Spleen
4	chr2:113992000-113997000	Weak transcription	Esophagus	oesophagus
5	chr2:113992000-113997000	Weak transcription	Fetal Heart	heart
6	chr2:113992000-113997000	Weak transcription	Right Atrium	heart
7	chr2:113992000-113997400	Weak transcription	Left Ventricle	heart
8	chr2:113992000-113997400	Weak transcription	Right Ventricle	heart
9	chr2:113993400-113996800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:113993400-113997000	Weak transcription	Liver	Liver
11	chr2:113993400-113997000	Weak transcription	Brain Anterior Caudate	brain
12	chr2:113993400-113997000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:113993400-113997000	Weak transcription	Brain Substantia Nigra	brain
14	chr2:113993400-113997200	Weak transcription	Stomach Mucosa	stomach
15	chr2:113993400-113997400	Weak transcription	HUVEC	blood vessel
16	chr2:113993400-114000000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:113993600-113997000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:113993600-113997000	Weak transcription	Fetal Intestine Small	intestine
20	chr2:113993600-113997400	Weak transcription	Brain Angular Gyrus	brain
21	chr2:113993800-113997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:113994200-114002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:113994400-113997000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:113994400-113997000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:113994400-113997000	Weak transcription	Fetal Thymus	thymus
27	chr2:113994400-113997200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:113994400-113997600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:113994400-113997800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:113994600-113996400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:113994600-113996800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:113994600-113997000	Weak transcription	Colonic Mucosa	Colon
33	chr2:113994600-113997000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:113994600-113997000	Weak transcription	Fetal Intestine Large	intestine
35	chr2:113994600-113997400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:113994600-113997400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:113994600-113998000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:113994600-113998000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:113994600-114000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:113994800-113996400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:113994800-113996400	Enhancers	HepG2	liver
42	chr2:113994800-113996800	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:113994800-113997400	Weak transcription	Fetal Stomach	stomach
44	chr2:113994800-113997600	Weak transcription	Ovary	ovary
45	chr2:113994800-113998000	Weak transcription	Fetal Brain Female	brain
46	chr2:113994800-113998600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:113995000-113997000	Weak transcription	Lung	lung
49	chr2:113995000-113998200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:113995000-113998800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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