Variant report

Variant	rs2305133
Chromosome Location	chr2:113956821-113956822
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113931492..113932996-chr2:113955583..113957836,2	MCF-7	breast:
2	chr2:113894199..113895178-chr2:113956349..113957482,7	MCF-7	breast:
3	chr2:113895684..113896622-chr2:113956462..113957445,3	MCF-7	breast:
4	chr2:113956422..113958569-chr2:113991553..113994219,2	MCF-7	breast:
5	chr2:113949542..113953586-chr2:113955251..113958622,5	MCF-7	breast:
6	chr2:113895331..113896490-chr2:113956383..113957293,5	MCF-7	breast:
7	chr2:113956459..113959352-chr2:113984317..113985947,2	K562	blood:
8	chr2:113956609..113958908-chr2:113996941..113999634,4	MCF-7	breast:
9	chr2:113837862..113838404-chr2:113956604..113957377,3	MCF-7	breast:
10	chr2:113955248..113957880-chr2:113994557..113996875,2	MCF-7	breast:
11	chr2:113933537..113935192-chr2:113956517..113958039,2	MCF-7	breast:
12	chr2:113947298..113949233-chr2:113956219..113958532,2	MCF-7	breast:
13	chr2:113894243..113895050-chr2:113956611..113957124,2	MCF-7	breast:
14	chr2:61404133..61405069-chr2:113956037..113956958,2	HCT-116	colon:
15	chr2:113912322..113918193-chr2:113953978..113958305,10	MCF-7	breast:
16	chr2:113913769..113918338-chr2:113954843..113958220,11	MCF-7	breast:
17	chr2:113950663..113952350-chr2:113953925..113956890,2	K562	blood:
18	chr2:113837234..113838476-chr2:113956411..113957308,6	MCF-7	breast:
19	chr2:113914412..113914976-chr2:113956450..113956998,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000234174	Chromatin interaction
ENSG00000258395	Chromatin interaction
ENSG00000125637	Chromatin interaction
ENSG00000173209	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10175462	0.82[ASN][1000 genomes]
rs10206269	0.81[ASN][1000 genomes]
rs1110839	0.81[ASN][1000 genomes]
rs11123170	0.82[ASN][1000 genomes]
rs11123172	0.82[ASN][1000 genomes]
rs12612729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619508	0.84[EUR][1000 genomes]
rs12620738	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2015769	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2019137	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241978	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863243	0.82[ASN][1000 genomes]
rs3748916	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3811059	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828188	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828189	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4848318	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849169	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849176	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4849177	0.81[ASN][1000 genomes]
rs4849179	0.82[ASN][1000 genomes]
rs4849183	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62160781	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6707386	0.82[ASN][1000 genomes]
rs6755040	0.82[ASN][1000 genomes]
rs6755639	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs731834	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7421852	0.81[ASN][1000 genomes]
rs7563094	0.82[ASN][1000 genomes]
rs7578633	0.82[ASN][1000 genomes]
rs895412	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs902695	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs902696	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874900	chr2:113948378-113967990	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2305133	PAX8	cis	Esophagus Muscularis	GTEx
rs2305133	PAX8	cis	Adipose Subcutaneous	GTEx
rs2305133	AC016683.6	cis	Esophagus Muscularis	GTEx
rs2305133	AC016683.6	cis	Nerve Tibial	GTEx
rs2305133	AC016683.6	cis	Artery Tibial	GTEx
rs2305133	AC016683.6	cis	Esophagus Mucosa	GTEx
rs2305133	PAX8	cis	lung	GTEx
rs2305133	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs2305133	AC016683.6	cis	lung	GTEx
rs2305133	AC016683.6	cis	Muscle Skeletal	GTEx
rs2305133	AC016683.6	cis	Whole Blood	GTEx
rs2305133	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs2305133	PAX8	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113940000-113961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:113942800-113961000	Strong transcription	Dnd41	blood
3	chr2:113947400-113961000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:113947800-113959600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:113947800-113960600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:113948600-113961000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:113949000-113961200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:113950000-113961000	Strong transcription	Primary T cells from cord blood	blood
9	chr2:113952600-113957800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:113954000-113957000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:113955800-113957000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:113955800-113957200	Weak transcription	Primary B cells from cord blood	blood
13	chr2:113955800-113957600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:113955800-113958000	Weak transcription	K562	blood
15	chr2:113955800-113959200	Enhancers	Stomach Mucosa	stomach
16	chr2:113956000-113957000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:113956000-113957000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr2:113956000-113957000	Active TSS	Brain Angular Gyrus	brain
19	chr2:113956000-113957000	Active TSS	Brain Anterior Caudate	brain
20	chr2:113956000-113957000	Active TSS	Duodenum Mucosa	Duodenum
21	chr2:113956000-113957000	Enhancers	Fetal Brain Male	brain
22	chr2:113956000-113957000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr2:113956000-113957000	Active TSS	A549	lung
24	chr2:113956000-113957000	Active TSS	Hela-S3	cervix
25	chr2:113956000-113957200	Active TSS	H1 Cell Line	embryonic stem cell
26	chr2:113956000-113957200	Active TSS	H9 Cell Line	embryonic stem cell
27	chr2:113956000-113957200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:113956000-113957200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:113956000-113957200	Active TSS	Colonic Mucosa	Colon
30	chr2:113956000-113957200	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr2:113956000-113957200	Active TSS	Pancreas	Pancrea
32	chr2:113956000-113957400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:113956000-113957800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:113956000-113958200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:113956200-113957000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr2:113956200-113957000	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr2:113956200-113957000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:113956200-113957000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:113956200-113957000	Active TSS	Brain Hippocampus Middle	brain
40	chr2:113956200-113957000	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr2:113956200-113957000	Enhancers	Fetal Heart	heart
42	chr2:113956200-113957000	Active TSS	Fetal Intestine Small	intestine
43	chr2:113956200-113957000	Active TSS	Fetal Lung	lung
44	chr2:113956200-113957000	Active TSS	Left Ventricle	heart
45	chr2:113956200-113957000	Active TSS	Placenta Amnion	Placenta Amnion
46	chr2:113956200-113957000	Active TSS	Osteobl	bone
47	chr2:113956200-113957200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr2:113956200-113957200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:113956200-113957200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:113956200-113957200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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