Variant report

Variant	rs3811059
Chromosome Location	chr2:113962071-113962072
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113956911..113959239-chr2:113960727..113963043,2	MCF-7	breast:
2	chr2:113958810..113962275-chr2:113967321..113970700,3	K562	blood:
3	chr2:113959536..113962611-chr2:113992413..113994769,3	K562	blood:
4	chr2:113960268..113963135-chr2:113993103..113996129,3	MCF-7	breast:
5	chr2:113960427..113963298-chr2:114003216..114006590,3	MCF-7	breast:
6	chr2:113836433..113838367-chr2:113961484..113963853,2	MCF-7	breast:
7	chr2:113961854..113963541-chr2:113993212..113994812,2	MCF-7	breast:
8	chr2:113960353..113963202-chr2:113996629..113998923,2	K562	blood:
9	chr2:113894549..113895054-chr2:113961608..113962495,2	MCF-7	breast:
10	chr2:113837662..113838271-chr2:113961226..113962104,2	MCF-7	breast:
11	chr2:113881134..113884097-chr2:113960459..113963321,2	K562	blood:
12	chr2:113955184..113958187-chr2:113960029..113962112,5	MCF-7	breast:
13	chr2:113961603..113962131-chr2:114147652..114148320,2	K562	blood:
14	chr2:113961213..113962188-chr2:114127876..114128919,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258395	Chromatin interaction
ENSG00000125637	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000189223	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	0.85[ASN][1000 genomes]
rs10206269	0.84[ASN][1000 genomes]
rs1110839	0.86[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11123170	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11123172	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12612729	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619508	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12620738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015769	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2019137	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241978	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276561	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305133	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2863243	0.85[ASN][1000 genomes]
rs3748916	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3828188	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3828189	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4848318	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849169	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849176	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849177	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4849179	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4849181	0.81[ASN][1000 genomes]
rs4849183	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62160781	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707386	0.85[ASN][1000 genomes]
rs6751201	0.89[JPT][hapmap]
rs6755040	0.85[ASN][1000 genomes]
rs6755639	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs731834	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7421852	0.84[ASN][1000 genomes]
rs7563094	0.85[ASN][1000 genomes]
rs7578633	0.85[ASN][1000 genomes]
rs7589901	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs874898	0.94[JPT][hapmap]
rs895412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs902695	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs902696	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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
rs3811059	AC016683.6	cis	Whole Blood	GTEx
rs3811059	PAX8	cis	Esophagus Mucosa	GTEx
rs3811059	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs3811059	AC016683.6	cis	Esophagus Mucosa	GTEx
rs3811059	AC016683.6	cis	Nerve Tibial	GTEx
rs3811059	AC016683.6	cis	Esophagus Muscularis	GTEx
rs3811059	AC016683.6	cis	Artery Tibial	GTEx
rs3811059	PAX8	cis	Adipose Subcutaneous	GTEx
rs3811059	AC016683.6	cis	lung	GTEx
rs3811059	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs3811059	PAX8	cis	Esophagus Muscularis	GTEx
rs3811059	PAX8	cis	lung	GTEx
rs3811059	AC016683.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113956800-113962200	Strong transcription	GM12878-XiMat	blood
2	chr2:113957200-113969000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:113957200-113969000	Weak transcription	Right Atrium	heart
4	chr2:113957400-113967000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:113957400-113967800	Weak transcription	Adipose Nuclei	Adipose
6	chr2:113957400-113969000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:113958000-113962200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:113958000-113975200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:113958200-113966400	Weak transcription	HSMMtube	muscle
11	chr2:113958600-113962600	Enhancers	A549	lung
12	chr2:113959000-113962400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:113959000-113966600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:113959200-113968800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:113959200-113968800	Weak transcription	K562	blood
16	chr2:113959600-113967000	Weak transcription	Colonic Mucosa	Colon
17	chr2:113959600-113967600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:113959800-113962200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:113959800-113962400	Enhancers	HepG2	liver
20	chr2:113960400-113963400	Weak transcription	Lung	lung
21	chr2:113960400-113963600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:113960600-113963800	Weak transcription	Esophagus	oesophagus
23	chr2:113960600-113966200	Weak transcription	Fetal Stomach	stomach
24	chr2:113960600-113975200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:113960800-113963400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:113960800-113968600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr2:113960800-113969600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:113960800-113974600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:113960800-113975000	Weak transcription	Liver	Liver
30	chr2:113961000-113963800	Weak transcription	Placenta	Placenta
31	chr2:113961000-113966200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:113961000-113966200	Weak transcription	HSMM	muscle
33	chr2:113961000-113967200	Weak transcription	Thymus	Thymus
34	chr2:113961000-113968400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr2:113961200-113963400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:113961400-113962200	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr2:113961400-113962400	Enhancers	Fetal Thymus	thymus
38	chr2:113961600-113962200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:113961600-113962200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:113961600-113962400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr2:113961600-113962400	Enhancers	Fetal Intestine Large	intestine
42	chr2:113961600-113962400	Genic enhancers	Fetal Intestine Small	intestine
43	chr2:113961600-113962600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr2:113961600-113962600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr2:113961600-113962600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:113961600-113963200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr2:113961800-113962200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr2:113961800-113962200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr2:113961800-113962200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr2:113961800-113962200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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