Variant report

Variant	rs4848329
Chromosome Location	chr2:114043454-114043455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114034404..114036046-chr2:114042741..114044743,2	K562	blood:

Variant related genes	Relation type
ENSG00000125618	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10201645	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10209795	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123174	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123175	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679928	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11683025	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687706	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688620	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11889663	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12467534	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12989922	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002606	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13022812	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385108	0.82[AMR][1000 genomes]
rs13388160	0.85[AMR][1000 genomes]
rs17626434	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17626470	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34657362	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4091938	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4848324	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848325	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848326	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848327	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848328	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848330	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4849191	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4849192	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849194	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6753679	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6760462	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6760648	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv961872	chr2:114041837-114061641	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4848329	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs4848329	PAX8	cis	Nerve Tibial	GTEx
rs4848329	AC016683.6	cis	Whole Blood	GTEx
rs4848329	AC016683.6	cis	Nerve Tibial	GTEx
rs4848329	AC016683.6	cis	Muscle Skeletal	GTEx
rs4848329	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs4848329	PAX8	cis	Adipose Subcutaneous	GTEx
rs4848329	PAX8	cis	lung	GTEx
rs4848329	AC016683.6	cis	Esophagus Mucosa	GTEx
rs4848329	PAX8	cis	Esophagus Muscularis	GTEx
rs4848329	PAX8	cis	Esophagus Mucosa	GTEx
rs4848329	AC016683.6	cis	lung	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114036600-114043800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:114037400-114043600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:114037600-114043800	Enhancers	HMEC	breast
4	chr2:114038200-114043800	Enhancers	Fetal Intestine Large	intestine
5	chr2:114038400-114043600	Enhancers	Fetal Intestine Small	intestine
6	chr2:114038600-114043600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:114038600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:114039000-114043800	Enhancers	HSMM	muscle
9	chr2:114039600-114043600	Enhancers	HSMMtube	muscle
10	chr2:114039600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:114039800-114043600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:114040600-114043600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:114040600-114043600	Enhancers	Colon Smooth Muscle	Colon
14	chr2:114040600-114043600	Enhancers	NHDF-Ad	bronchial
15	chr2:114040600-114047000	Enhancers	Liver	Liver
16	chr2:114040600-114047800	Weak transcription	Gastric	stomach
17	chr2:114041000-114043600	Enhancers	Rectal Smooth Muscle	rectum
18	chr2:114041200-114043600	Enhancers	NHEK	skin
19	chr2:114041400-114043800	Enhancers	A549	lung
20	chr2:114041600-114043600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:114042200-114044200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:114042200-114045400	Weak transcription	Stomach Mucosa	stomach
23	chr2:114042200-114046000	Weak transcription	Brain Anterior Caudate	brain
24	chr2:114042200-114046200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:114042400-114043600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr2:114042400-114043600	Enhancers	NH-A	brain
27	chr2:114042400-114044600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:114042400-114045000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:114042400-114045200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:114042600-114043600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:114042600-114043600	Weak transcription	HepG2	liver
32	chr2:114042600-114048600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:114043000-114043600	Enhancers	Spleen	Spleen
34	chr2:114043200-114048800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:114043400-114043600	Bivalent Enhancer	Osteobl	bone
36	chr2:114043400-114043800	Enhancers	Stomach Smooth Muscle	stomach
37	chr2:114043400-114044200	Enhancers	Pancreas	Pancrea
38	chr2:114043400-114047800	Weak transcription	Lung	lung

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