Variant report

Variant	rs4849177
Chromosome Location	chr2:113982584-113982585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113982408-113988487	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113982222..113985690-chr2:113985752..113988361,3	MCF-7	breast:
2	chr2:113978254..113980033-chr2:113981611..113983261,2	MCF-7	breast:
3	chr2:113976625..113978334-chr2:113981431..113983858,2	K562	blood:
4	chr2:113976337..113978334-chr2:113981431..113983858,3	K562	blood:

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000125618	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 29 )

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

rs_ID	r²[population]
rs10175462	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10206269	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1110839	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11123170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12612729	0.81[ASN][1000 genomes]
rs12619508	0.86[ASN][1000 genomes]
rs12620738	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2015769	0.80[ASN][1000 genomes]
rs2019137	0.88[ASN][1000 genomes]
rs2276561	0.81[ASN][1000 genomes]
rs2305133	0.81[ASN][1000 genomes]
rs2863243	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3811059	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3828188	0.81[ASN][1000 genomes]
rs4849176	0.93[ASN][1000 genomes]
rs4849179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849181	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849183	0.90[ASN][1000 genomes]
rs6707386	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6751201	0.82[JPT][hapmap]
rs6755040	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6755639	0.93[ASN][1000 genomes]
rs731834	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7421852	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7563094	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7576384	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7578633	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7589901	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs874898	0.88[JPT][hapmap]
rs895412	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs902695	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs902696	0.90[CHB][hapmap];0.94[JPT][hapmap]

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:29)

SNP	Gene	Cis/trans	Tissue	Source
rs4849177	PAX8	cis	Artery Aorta	GTEx
rs4849177	AC016683.6	cis	Muscle Skeletal	GTEx
rs4849177	PAX8	cis	Lymphoblastoid	GTEx
rs4849177	AC016683.6	cis	Whole Blood	GTEx
rs4849177	LOC654433	cis	lesional skin	skin_eQTL
rs4849177	PAX8	cis	lung	GTEx
rs4849177	PAX8	cis	multi-tissue	Pritchard
rs4849177	PSD4	cis	multi-tissue	Pritchard
rs4849177	AC016683.6	cis	Esophagus Muscularis	GTEx
rs4849177	AC016683.6	cis	Stomach	GTEx
rs4849177	PAX8	cis	Nerve Tibial	GTEx
rs4849177	AC016683.6	cis	lung	GTEx
rs4849177	PAX8	cis	Esophagus Mucosa	GTEx
rs4849177	PAX8	cis	Adipose Subcutaneous	GTEx
rs4849177	PAX8	cis	Skin Sun Exposed Lower leg	GTEx
rs4849177	AC016683.6	cis	Nerve Tibial	GTEx
rs4849177	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs4849177	AC016683.6	cis	Esophagus Mucosa	GTEx
rs4849177	LOC654433	cis	Lymphoblastoid	GTEx
rs4849177	AC016683.6	cis	Artery Tibial	GTEx
rs4849177	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs4849177	AC016683.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4849177	AC016683.6	cis	Heart Left Ventricle	GTEx
rs4849177	PAX8	cis	Esophagus Muscularis	GTEx
rs4849177	PAX8	cis	Whole Blood	GTEx
rs4849177	PAX8	cis	Artery Tibial	GTEx
rs4849177	AC016683.6	cis	Artery Aorta	GTEx
rs4849177	PAX8	cis	lesional skin	skin_eQTL
rs4849177	Hs.169006	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:113970600-113982600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:113970800-113983000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:113972200-113982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:113975600-113983600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:113975800-113982600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:113975800-113983000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:113975800-113983200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:113976400-113982800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:113976600-113983200	Weak transcription	Fetal Lung	lung
11	chr2:113977400-113985600	Weak transcription	Gastric	stomach
12	chr2:113977600-113982600	Weak transcription	NH-A	brain
13	chr2:113977600-113983000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:113977800-113982600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:113977800-113982600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:113977800-113983600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:113978000-113982600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:113978000-113982600	Weak transcription	Brain Anterior Caudate	brain
19	chr2:113978000-113983000	Weak transcription	Osteobl	bone
20	chr2:113978000-113983200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:113978000-113983200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:113978000-113986400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:113978000-113987600	Weak transcription	Esophagus	oesophagus
24	chr2:113978200-113983000	Weak transcription	Fetal Stomach	stomach
25	chr2:113978200-113983200	Weak transcription	Fetal Intestine Small	intestine
26	chr2:113978200-113987200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr2:113978200-113991800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:113978400-113983000	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:113978400-113983600	Weak transcription	Lung	lung
30	chr2:113978400-113983600	Weak transcription	Pancreas	Pancrea
31	chr2:113978600-113983000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:113978600-113984600	Genic enhancers	Fetal Kidney	kidney
33	chr2:113978800-113982600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:113978800-113986200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:113979000-113982600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:113979000-113982600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:113979600-113982800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr2:113980000-113982600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:113980000-113982800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:113980000-113982800	Weak transcription	Stomach Mucosa	stomach
41	chr2:113980000-113983200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:113980200-113982600	Weak transcription	A549	lung
43	chr2:113980200-113983200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:113980200-113991600	Weak transcription	Spleen	Spleen
45	chr2:113981200-113982600	Weak transcription	HepG2	liver
46	chr2:113982000-113983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:113982400-113983200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:113982400-113984200	Enhancers	Fetal Intestine Large	intestine

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