Variant report

Variant	rs2019137
Chromosome Location	chr2:113973632-113973633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113973127..113974813-chr2:113991728..113993751,2	MCF-7	breast:
2	chr2:113973621..113980487-chr2:113991287..113996231,8	K562	blood:
3	chr2:113973569..113976891-chr2:113987783..113991644,3	MCF-7	breast:
4	chr2:113973502..113975289-chr2:113978788..113980308,2	K562	blood:
5	chr2:113968914..113973967-chr2:113991743..113995400,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189223	Chromatin interaction
ENSG00000125618	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10175462	0.89[ASN][1000 genomes]
rs10206269	0.88[ASN][1000 genomes]
rs1110839	0.88[ASN][1000 genomes]
rs11123170	0.89[ASN][1000 genomes]
rs11123172	0.89[ASN][1000 genomes]
rs12612729	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12619508	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12620738	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2015769	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241978	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276561	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305133	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2863243	0.89[ASN][1000 genomes]
rs3748916	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3811059	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3828188	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828189	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4848318	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849169	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849174	0.82[ASN][1000 genomes]
rs4849176	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4849177	0.88[ASN][1000 genomes]
rs4849179	0.89[ASN][1000 genomes]
rs4849181	0.85[ASN][1000 genomes]
rs4849183	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62160781	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6707386	0.89[ASN][1000 genomes]
rs6755040	0.89[ASN][1000 genomes]
rs6755639	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs731834	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7421852	0.88[ASN][1000 genomes]
rs7563094	0.89[ASN][1000 genomes]
rs7576384	0.81[ASN][1000 genomes]
rs7578633	0.89[ASN][1000 genomes]
rs7589901	0.83[ASN][1000 genomes]
rs895412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902695	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs902696	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2019137	AC016683.6	cis	Esophagus Muscularis	GTEx
rs2019137	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs2019137	PAX8	cis	Esophagus Muscularis	GTEx
rs2019137	PAX8	cis	lung	GTEx
rs2019137	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs2019137	AC016683.6	cis	Artery Tibial	GTEx
rs2019137	PAX8	cis	Adipose Subcutaneous	GTEx
rs2019137	AC016683.6	cis	Esophagus Mucosa	GTEx
rs2019137	AC016683.6	cis	lung	GTEx
rs2019137	AC016683.6	cis	Muscle Skeletal	GTEx
rs2019137	AC016683.6	cis	Nerve Tibial	GTEx
rs2019137	AC016683.6	cis	Whole Blood	GTEx
rs2019137	PAX8	cis	Esophagus Mucosa	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:113958000-113975200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:113960600-113975200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:113960800-113974600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:113960800-113975000	Weak transcription	Liver	Liver
6	chr2:113962200-113974800	Weak transcription	GM12878-XiMat	blood
7	chr2:113962600-113974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:113967600-113975200	Weak transcription	Gastric	stomach
9	chr2:113969400-113974800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:113969400-113975400	Weak transcription	Right Ventricle	heart
11	chr2:113969600-113974800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:113969600-113974800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:113969800-113974600	Weak transcription	Brain Substantia Nigra	brain
14	chr2:113969800-113974800	Weak transcription	Fetal Thymus	thymus
15	chr2:113970000-113974400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:113970000-113974400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:113970000-113974400	Weak transcription	HSMMtube	muscle
18	chr2:113970000-113975000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:113970000-113975000	Weak transcription	Osteobl	bone
20	chr2:113970000-113975400	Weak transcription	Stomach Mucosa	stomach
21	chr2:113970200-113974600	Weak transcription	HSMM	muscle
22	chr2:113970400-113974600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:113970400-113974800	Weak transcription	Small Intestine	intestine
24	chr2:113970400-113975000	Weak transcription	Hela-S3	cervix
25	chr2:113970400-113975600	Weak transcription	NHLF	lung
26	chr2:113970600-113973800	Weak transcription	Fetal Intestine Large	intestine
27	chr2:113970600-113973800	Weak transcription	Fetal Intestine Small	intestine
28	chr2:113970600-113973800	Weak transcription	Left Ventricle	heart
29	chr2:113970600-113974400	Weak transcription	NH-A	brain
30	chr2:113970600-113974600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:113970600-113974600	Weak transcription	Colonic Mucosa	Colon
32	chr2:113970600-113974600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr2:113970600-113974800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:113970600-113975200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:113970600-113975200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:113970600-113982600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:113970800-113974000	Weak transcription	Lung	lung
38	chr2:113970800-113974000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:113970800-113974600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:113970800-113974600	Weak transcription	Pancreas	Pancrea
41	chr2:113970800-113974800	Weak transcription	Brain Anterior Caudate	brain
42	chr2:113970800-113975000	Weak transcription	Right Atrium	heart
43	chr2:113970800-113975200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:113970800-113975400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:113970800-113975600	Weak transcription	NHDF-Ad	bronchial
46	chr2:113970800-113983000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:113971000-113974000	Weak transcription	Adipose Nuclei	Adipose
48	chr2:113971000-113974800	Weak transcription	Fetal Heart	heart
49	chr2:113971000-113974800	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:113971200-113974600	Weak transcription	Fetal Lung	lung

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