Variant report

Variant	rs1139015
Chromosome Location	chr2:113996888-113996889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113996846-113997237	ECC-1	luminal epithelium:	n/a	n/a
2	NR3C1	chr2:113996869-113997218	A549	lung:	n/a	n/a
3	NR3C1	chr2:113996769-113997247	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113952804..113954880-chr2:113996400..113999228,2	MCF-7	breast:
2	chr2:113958931..113961853-chr2:113995609..113998129,2	K562	blood:
3	chr2:113970934..113973261-chr2:113995727..113997421,2	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-1	chr2:113996666-113998402	ENSG00000189223
2	lnc-PSD4-1	chr2:113996666-113997267	ENSG00000189223
3	lnc-PSD4-1	chr2:113996666-113997485	ENSG00000189223
4	lnc-PSD4-1	chr2:113996666-113997165	ENSG00000189223
5	lnc-PSD4-1	chr2:113996666-113998419	NONHSAT073761

No data

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

Extended variants
information (count: 7 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs35129549	0.83[AMR][1000 genomes]
rs35920363	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3762497	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6734596	0.82[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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs1139015	PAX8	cis	Adipose Subcutaneous	GTEx
rs1139015	AC016683.6	cis	Skin Sun Exposed Lower leg	GTEx
rs1139015	AC016683.6	cis	Esophagus Mucosa	GTEx
rs1139015	AC016683.6	cis	Stomach	GTEx
rs1139015	AC016683.6	cis	Esophagus Muscularis	GTEx
rs1139015	PAX8	cis	Artery Tibial	GTEx
rs1139015	PAX8	cis	Skin Sun Exposed Lower leg	GTEx
rs1139015	PAX8	cis	Whole Blood	GTEx
rs1139015	PAX8	cis	Esophagus Mucosa	GTEx
rs1139015	PAX8	Cis_1M	lymphoblastoid	RTeQTL
rs1139015	PAX8	cis	Esophagus Muscularis	GTEx
rs1139015	AC016683.6	cis	Whole Blood	GTEx
rs1139015	AC016683.6	cis	Heart Left Ventricle	GTEx
rs1139015	AC016683.6	cis	Artery Tibial	GTEx
rs1139015	AC016683.6	cis	Artery Aorta	GTEx
rs1139015	RP11-65I12.1	cis	Esophagus Muscularis	GTEx
rs1139015	AC016683.6	cis	Nerve Tibial	GTEx
rs1139015	PAX8	cis	Nerve Tibial	GTEx
rs1139015	PAX8	cis	lung	GTEx
rs1139015	AC016683.6	cis	lung	GTEx
rs1139015	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs1139015	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs1139015	RP11-65I12.1	cis	Esophagus Mucosa	GTEx
rs1139015	AC016683.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:92 , 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	chr2:113993400-113997000	Weak transcription	Liver	Liver
10	chr2:113993400-113997000	Weak transcription	Brain Anterior Caudate	brain
11	chr2:113993400-113997000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:113993400-113997000	Weak transcription	Brain Substantia Nigra	brain
13	chr2:113993400-113997200	Weak transcription	Stomach Mucosa	stomach
14	chr2:113993400-113997400	Weak transcription	HUVEC	blood vessel
15	chr2:113993400-114000000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:113993600-113997000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:113993600-113997000	Weak transcription	Fetal Intestine Small	intestine
19	chr2:113993600-113997400	Weak transcription	Brain Angular Gyrus	brain
20	chr2:113993800-113997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:113994200-114002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:113994400-113997000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:113994400-113997000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:113994400-113997000	Weak transcription	Fetal Thymus	thymus
26	chr2:113994400-113997200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:113994400-113997600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:113994400-113997800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:113994600-113997000	Weak transcription	Colonic Mucosa	Colon
30	chr2:113994600-113997000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:113994600-113997000	Weak transcription	Fetal Intestine Large	intestine
32	chr2:113994600-113997400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:113994600-113997400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:113994600-113998000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:113994600-113998000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:113994600-114000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:113994800-113997400	Weak transcription	Fetal Stomach	stomach
38	chr2:113994800-113997600	Weak transcription	Ovary	ovary
39	chr2:113994800-113998000	Weak transcription	Fetal Brain Female	brain
40	chr2:113994800-113998600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:113995000-113997000	Weak transcription	Lung	lung
43	chr2:113995000-113998200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:113995000-113998800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:113995200-113997000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:113995200-113997200	Weak transcription	Osteobl	bone
48	chr2:113995200-113997600	Enhancers	Adipose Nuclei	Adipose
49	chr2:113995200-113997800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:113995200-114000000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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