Variant report

Variant	rs4849176
Chromosome Location	chr2:113977936-113977937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113967701..113970551-chr2:113977130..113979448,2	K562	blood:
2	chr2:113973621..113980487-chr2:113991287..113996231,8	K562	blood:

Variant related genes	Relation type
ENSG00000125618	Chromatin interaction
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10175462	0.95[ASN][1000 genomes]
rs10206269	0.94[ASN][1000 genomes]
rs1110839	0.94[ASN][1000 genomes]
rs11123170	0.95[ASN][1000 genomes]
rs11123172	0.95[ASN][1000 genomes]
rs12612729	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12619508	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12620738	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2015769	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2019137	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241978	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2276561	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2305133	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2863243	0.95[ASN][1000 genomes]
rs3748916	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811059	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3828188	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3828189	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4848318	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4849169	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4849177	0.93[ASN][1000 genomes]
rs4849179	0.95[ASN][1000 genomes]
rs4849181	0.91[ASN][1000 genomes]
rs4849183	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62160781	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6707386	0.95[ASN][1000 genomes]
rs6755040	0.95[ASN][1000 genomes]
rs6755639	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731834	0.87[AMR][1000 genomes];0.89[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	0.89[ASN][1000 genomes]
rs895412	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs902695	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs902696	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs4849176	PAX8	cis	Esophagus Mucosa	GTEx
rs4849176	AC016683.6	cis	Stomach	GTEx
rs4849176	AC016683.6	cis	Esophagus Mucosa	GTEx
rs4849176	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs4849176	PAX8	Cis_1M	lymphoblastoid	RTeQTL
rs4849176	PAX8	cis	Nerve Tibial	GTEx
rs4849176	PAX8	cis	Adipose Subcutaneous	GTEx
rs4849176	AC016683.6	cis	lung	GTEx
rs4849176	AC016683.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4849176	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs4849176	PAX8	cis	Whole Blood	GTEx
rs4849176	PAX8	cis	lung	GTEx
rs4849176	AC016683.6	cis	Whole Blood	GTEx
rs4849176	AC016683.6	cis	Muscle Skeletal	GTEx
rs4849176	AC016683.6	cis	Artery Tibial	GTEx
rs4849176	PAX8	cis	Skin Sun Exposed Lower leg	GTEx
rs4849176	AC016683.6	cis	Esophagus Muscularis	GTEx
rs4849176	AC016683.6	cis	Heart Left Ventricle	GTEx
rs4849176	PAX8	cis	Esophagus Muscularis	GTEx
rs4849176	AC016683.6	cis	Nerve Tibial	GTEx

Chromatin state (count:70 , 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	chr2:113970600-113982600	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	chr2:113973200-113978200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:113973800-113978200	Enhancers	Fetal Intestine Small	intestine
7	chr2:113973800-113979400	Enhancers	Fetal Intestine Large	intestine
8	chr2:113974000-113978200	Enhancers	Adipose Nuclei	Adipose
9	chr2:113974000-113978400	Enhancers	Lung	lung
10	chr2:113974000-113980000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:113974400-113978800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:113974400-113979000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:113974600-113978000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr2:113974600-113978000	Enhancers	Placenta	Placenta
15	chr2:113974600-113978200	Enhancers	Spleen	Spleen
16	chr2:113974600-113978200	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr2:113974600-113978400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr2:113974600-113978400	Enhancers	Pancreas	Pancrea
19	chr2:113974600-113979600	Enhancers	Primary hematopoietic stem cells	blood
20	chr2:113974800-113978000	Enhancers	Brain Anterior Caudate	brain
21	chr2:113974800-113978000	Enhancers	HMEC	breast
22	chr2:113974800-113978400	Enhancers	Fetal Muscle Leg	muscle
23	chr2:113975000-113978000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr2:113975000-113978000	Enhancers	Osteobl	bone
25	chr2:113975000-113979200	Enhancers	Hela-S3	cervix
26	chr2:113975200-113979000	Flanking Active TSS	A549	lung
27	chr2:113975400-113978200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:113975400-113980000	Enhancers	Stomach Mucosa	stomach
29	chr2:113975600-113978000	Enhancers	NHDF-Ad	bronchial
30	chr2:113975600-113978000	Enhancers	NHLF	lung
31	chr2:113975600-113983600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:113975800-113978000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:113975800-113978000	Weak transcription	Fetal Stomach	stomach
34	chr2:113975800-113978000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr2:113975800-113978400	Enhancers	Colonic Mucosa	Colon
36	chr2:113975800-113980000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:113975800-113982600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:113975800-113983000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:113975800-113983200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:113976000-113978400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:113976000-113978600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:113976000-113980000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:113976400-113978000	Enhancers	Fetal Kidney	kidney
44	chr2:113976400-113982800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:113976600-113980000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr2:113976600-113983200	Weak transcription	Fetal Lung	lung
47	chr2:113976800-113978200	Weak transcription	Right Ventricle	heart
48	chr2:113977200-113978000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:113977200-113978000	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr2:113977200-113978000	Enhancers	Primary T cells from cord blood	blood

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