Variant report

Variant	rs13021601
Chromosome Location	chr2:113191010-113191011
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13025468	0.84[AMR][1000 genomes]
rs13422242	0.96[EUR][1000 genomes]
rs34510112	0.82[EUR][1000 genomes]
rs6542056	0.98[EUR][1000 genomes]
rs6728112	0.81[EUR][1000 genomes]
rs6729910	0.84[AMR][1000 genomes]
rs6759275	0.84[AMR][1000 genomes]
rs71414642	0.89[EUR][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	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv1801285	chr2:113113618-113200081	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	esv3371480	chr2:113189306-113191854	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs13021601	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs13021601	RGPD8	cis	Heart Left Ventricle	GTEx
rs13021601	RGPD8	cis	Esophagus Mucosa	GTEx
rs13021601	RGPD8	cis	Thyroid	GTEx
rs13021601	ZC3H8	cis	Artery Tibial	GTEx
rs13021601	RGPD8	cis	lung	GTEx
rs13021601	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs13021601	RGPD8	cis	Nerve Tibial	GTEx
rs13021601	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs13021601	RGPD8	cis	Esophagus Muscularis	GTEx
rs13021601	RGPD8	cis	Artery Tibial	GTEx
rs13021601	RGPD8	cis	Muscle Skeletal	GTEx
rs13021601	RGPD8	cis	Artery Aorta	GTEx
rs13021601	RGPD8	cis	Adipose Subcutaneous	GTEx
rs13021601	RGPD8	cis	Whole Blood	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113189000-113191200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:113189000-113191200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:113189000-113191200	Active TSS	Liver	Liver
4	chr2:113189200-113191200	Active TSS	Osteobl	bone
5	chr2:113189400-113191200	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr2:113189400-113191200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:113189400-113191200	Active TSS	Colonic Mucosa	Colon
8	chr2:113189400-113191200	Active TSS	Hela-S3	cervix
9	chr2:113189400-113191200	Active TSS	HSMM	muscle
10	chr2:113189400-113191400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:113189600-113191200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr2:113189600-113191200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:113189600-113191200	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr2:113189600-113191200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr2:113189600-113191200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:113189600-113191200	Active TSS	Muscle Satellite Cultured Cells	--
17	chr2:113189600-113191200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:113189600-113191200	Active TSS	Brain Cingulate Gyrus	brain
19	chr2:113189600-113191200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr2:113189600-113191200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:113189600-113191200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr2:113189600-113191200	Active TSS	Stomach Smooth Muscle	stomach
23	chr2:113189600-113191200	Active TSS	GM12878-XiMat	blood
24	chr2:113189600-113191200	Active TSS	HMEC	breast
25	chr2:113189600-113191200	Active TSS	HSMMtube	muscle
26	chr2:113189600-113191200	Active TSS	HUVEC	blood vessel
27	chr2:113189600-113191200	Active TSS	NH-A	brain
28	chr2:113189600-113191200	Active TSS	NHEK	skin
29	chr2:113189600-113191400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:113189600-113191400	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr2:113189600-113191800	Active TSS	Brain Anterior Caudate	brain
32	chr2:113189600-113191800	Active TSS	Brain Hippocampus Middle	brain
33	chr2:113189600-113193000	Active TSS	HepG2	liver
34	chr2:113189800-113191200	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr2:113189800-113191200	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr2:113189800-113191200	Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr2:113189800-113191200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:113189800-113191200	Active TSS	Adipose Nuclei	Adipose
39	chr2:113189800-113191200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr2:113189800-113191200	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr2:113189800-113191200	Active TSS	Thymus	Thymus
42	chr2:113189800-113191200	Active TSS	A549	lung
43	chr2:113189800-113191200	Active TSS	Monocytes-CD14+_RO01746	blood
44	chr2:113189800-113191200	Active TSS	NHLF	lung
45	chr2:113189800-113191600	Active TSS	Fetal Brain Female	brain
46	chr2:113190000-113191200	Active TSS	H1 Cell Line	embryonic stem cell
47	chr2:113190000-113191200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:113190000-113191200	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:113190000-113191200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:113190000-113191200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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