Variant report

Variant	rs3738913
Chromosome Location	chr2:113994461-113994462
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	chr2:113994048-113994559	MCF-7	breast:	n/a	n/a
2	POLR2A	chr2:113994368-113994843	K562	blood:	n/a	n/a
3	NR3C1	chr2:113994210-113994667	A549	lung:	n/a	n/a
4	NR3C1	chr2:113994237-113994610	A549	lung:	n/a	n/a
5	POLR2A	chr2:113993953-113995641	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr2:113994161-113994725	K562	blood:	n/a	n/a
7	POLR2A	chr2:113992678-113994712	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:113993933-113995568	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr2:113994091-113994693	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113968914..113973967-chr2:113991743..113995400,6	MCF-7	breast:
2	chr2:113973621..113980487-chr2:113991287..113996231,8	K562	blood:

Variant related genes	Relation type
ENSG00000258395	TF binding region
PAX8-AS1	TF binding region
PAX8	TF binding region
ENSG00000125618	Chromatin interaction
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1015753	0.85[ASN][1000 genomes]
rs1021409	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1049137	0.80[ASN][1000 genomes]
rs12467324	0.90[EUR][1000 genomes]
rs12472361	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12998725	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2003986	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2166421	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2863242	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35222158	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4849178	0.92[ASN][1000 genomes]
rs4849180	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4849182	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4849186	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs745912	0.82[AMR][1000 genomes];0.92[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3738913	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs3738913	AC016683.6	cis	Whole Blood	GTEx
rs3738913	PAX8	cis	Whole Blood	GTEx
rs3738913	PAX8	cis	lung	GTEx
rs3738913	AC016683.6	cis	lung	GTEx
rs3738913	AC016683.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:95 , 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	chr2:113992000-113994800	Weak transcription	HepG2	liver
5	chr2:113992000-113997000	Weak transcription	Esophagus	oesophagus
6	chr2:113992000-113997000	Weak transcription	Fetal Heart	heart
7	chr2:113992000-113997000	Weak transcription	Right Atrium	heart
8	chr2:113992000-113997400	Weak transcription	Left Ventricle	heart
9	chr2:113992000-113997400	Weak transcription	Right Ventricle	heart
10	chr2:113992600-113994600	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr2:113992600-113994600	Active TSS	Brain Hippocampus Middle	brain
12	chr2:113992600-113994600	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr2:113992600-113994600	Active TSS	Fetal Intestine Large	intestine
14	chr2:113992600-113994800	Active TSS	Duodenum Mucosa	Duodenum
15	chr2:113992600-113995000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:113992600-113995000	Active TSS	HSMM	muscle
17	chr2:113992600-113995200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:113992600-113995200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:113992600-113995200	Active TSS	Osteobl	bone
20	chr2:113992600-113995400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr2:113992800-113994600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr2:113992800-113994600	Active TSS	Rectal Smooth Muscle	rectum
23	chr2:113992800-113995400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:113992800-113995600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:113993000-113994600	Active TSS	Primary monocytes fromperipheralblood	blood
26	chr2:113993000-113994600	Weak transcription	NHLF	lung
27	chr2:113993000-113995400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:113993200-113994600	Weak transcription	A549	lung
29	chr2:113993200-113995200	Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr2:113993400-113996800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:113993400-113997000	Weak transcription	Liver	Liver
32	chr2:113993400-113997000	Weak transcription	Brain Anterior Caudate	brain
33	chr2:113993400-113997000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:113993400-113997000	Weak transcription	Brain Substantia Nigra	brain
35	chr2:113993400-113997200	Weak transcription	Stomach Mucosa	stomach
36	chr2:113993400-113997400	Weak transcription	HUVEC	blood vessel
37	chr2:113993400-114000000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:113993600-113997000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:113993600-113997000	Weak transcription	Fetal Intestine Small	intestine
41	chr2:113993600-113997400	Weak transcription	Brain Angular Gyrus	brain
42	chr2:113993800-113994600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:113993800-113994800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr2:113993800-113995400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr2:113993800-113997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:113994000-113994600	Flanking Active TSS	Lung	lung
47	chr2:113994000-113994800	Enhancers	Fetal Brain Female	brain
48	chr2:113994000-113995200	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:113994200-113994600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:113994200-113994600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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