Variant report

Variant	rs3748916
Chromosome Location	chr2:113984033-113984034
allele	A/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113983013..113984516-chr2:113998378..114000911,2	MCF-7	breast:
2	chr2:113983664..113985916-chr2:113988389..113990804,2	MCF-7	breast:
3	chr2:113983331..113985876-chr2:113990294..113993785,4	K562	blood:
4	chr2:113983505..113988046-chr2:113991447..113994622,4	MCF-7	breast:
5	chr2:113982222..113985690-chr2:113985752..113988361,3	MCF-7	breast:
6	chr2:113968640..113971575-chr2:113983814..113986609,4	MCF-7	breast:
7	chr2:113982814..113984707-chr2:113996972..113999644,2	K562	blood:
8	chr2:113978488..113981632-chr2:113983864..113986982,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000189223	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000258395	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10175462	0.95[ASN][1000 genomes]
rs10206269	0.94[ASN][1000 genomes]
rs1110839	0.87[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.94[ASN][1000 genomes]
rs11123170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11123172	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12612729	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12619508	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12620738	0.87[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1374161	0.81[ASW][hapmap]
rs1466018	0.87[ASW][hapmap]
rs2015769	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2019137	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241978	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2276561	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2305133	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2863243	0.95[ASN][1000 genomes]
rs3811059	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3828188	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3828189	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4848318	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4849169	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4849176	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4849179	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4849181	0.91[ASN][1000 genomes]
rs4849183	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62160781	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6707386	0.95[ASN][1000 genomes]
rs6751201	0.82[JPT][hapmap]
rs6755040	0.95[ASN][1000 genomes]
rs6755639	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731834	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7421852	0.94[ASN][1000 genomes]
rs7563094	0.95[ASN][1000 genomes]
rs7576384	0.86[ASN][1000 genomes]
rs7578633	0.95[ASN][1000 genomes]
rs7589901	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs874898	0.88[JPT][hapmap]
rs895412	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs902695	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs902696	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	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
rs3748916	PAX8	cis	Adipose Subcutaneous	GTEx
rs3748916	AC016683.6	cis	Heart Left Ventricle	GTEx
rs3748916	PAX8	cis	Esophagus Muscularis	GTEx
rs3748916	PAX8	cis	multi-tissue	Pritchard
rs3748916	AC016683.6	cis	Artery Tibial	GTEx
rs3748916	Hs.169006	cis	multi-tissue	Pritchard
rs3748916	PAX8	cis	parietal	SCAN
rs3748916	PAX8	cis	Esophagus Mucosa	GTEx
rs3748916	AC016683.6	cis	Whole Blood	GTEx
rs3748916	AC016683.6	cis	Esophagus Mucosa	GTEx
rs3748916	AC016683.6	cis	Skin Sun Exposed Lower leg	GTEx
rs3748916	PAX8	cis	Skin Sun Exposed Lower leg	GTEx
rs3748916	PAX8	cis	lung	GTEx
rs3748916	PAX8	cis	lymphoblastoid	seeQTL
rs3748916	AC016683.6	cis	Muscle Skeletal	GTEx
rs3748916	AC016683.6	cis	Esophagus Muscularis	GTEx
rs3748916	PAX8	cis	Nerve Tibial	GTEx
rs3748916	AC016683.6	cis	lung	GTEx
rs3748916	PAX8	cis	Whole Blood	GTEx
rs3748916	LOC654433	cis	cerebellum	SCAN
rs3748916	AC016683.6	cis	Nerve Tibial	GTEx
rs3748916	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs3748916	LOC654433	cis	parietal	SCAN
rs3748916	AC016683.6	cis	Stomach	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113977400-113985600	Weak transcription	Gastric	stomach
2	chr2:113978000-113986400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:113978000-113987600	Weak transcription	Esophagus	oesophagus
4	chr2:113978200-113987200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr2:113978200-113991800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:113978600-113984600	Genic enhancers	Fetal Kidney	kidney
7	chr2:113978800-113986200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:113980200-113991600	Weak transcription	Spleen	Spleen
9	chr2:113982400-113984200	Enhancers	Fetal Intestine Large	intestine
10	chr2:113982600-113984200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:113982600-113984200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:113982600-113984200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:113982600-113984200	Enhancers	Brain Anterior Caudate	brain
14	chr2:113982600-113984400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:113982600-113984400	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr2:113982600-113984600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:113982600-113984800	Enhancers	HepG2	liver
18	chr2:113982600-113987000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:113982600-113992600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr2:113982800-113990600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:113983000-113984200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:113983000-113984200	Enhancers	Fetal Muscle Leg	muscle
23	chr2:113983200-113984400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:113983200-113985600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:113983400-113984600	Enhancers	A549	lung
26	chr2:113983400-113987800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:113983400-113989000	Weak transcription	Stomach Mucosa	stomach
28	chr2:113983400-113989200	Enhancers	Primary hematopoietic stem cells	blood
29	chr2:113983400-113991600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:113983800-113984200	Weak transcription	Lung	lung
31	chr2:113983800-113984600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:113983800-113984800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:113983800-113989800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:113983800-113991800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:113984000-113984200	Enhancers	Fetal Lung	lung
36	chr2:113984000-113985000	Weak transcription	NH-A	brain
37	chr2:113984000-113985200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:113984000-113985800	Weak transcription	Fetal Brain Female	brain
39	chr2:113984000-113986600	Weak transcription	Fetal Intestine Small	intestine
40	chr2:113984000-113987400	Weak transcription	Pancreas	Pancrea
41	chr2:113984000-113987800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:113984000-113988400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:113984000-113990000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:113984000-113998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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