Variant report

Variant	rs2069506
Chromosome Location	chr12:58142854-58142855
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57913857..57916876-chr12:58140485..58143986,3	K562	blood:

Variant related genes	Relation type
ENSG00000175197	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1021469	0.82[EUR][1000 genomes]
rs10431505	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10431552	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10747783	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783847	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783848	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877011	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10877012	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877013	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877014	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877015	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877016	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877017	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877018	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877019	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172333	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172335	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172342	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172343	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172344	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172349	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172350	0.89[EUR][1000 genomes]
rs11172351	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1599932	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1875124	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2014886	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2069502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072052	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291617	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782130	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825079	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4646536	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56177740	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs703842	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs724834	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7965287	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8181644	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs923829	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9652011	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv826386	chr12:58135303-58150535	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv973963	chr12:58138245-58145482	Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2069506	CYP27B1	cis	Thyroid	GTEx
rs2069506	METTL21B	cis	lung	GTEx
rs2069506	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs2069506	METTL21B	cis	Esophagus Muscularis	GTEx
rs2069506	METTL21B	cis	Muscle Skeletal	GTEx
rs2069506	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs2069506	METTL21B	cis	Whole Blood	GTEx
rs2069506	XRCC6BP1	cis	Whole Blood	GTEx
rs2069506	METTL21B	cis	Adipose Subcutaneous	GTEx
rs2069506	METTL21B	cis	Heart Left Ventricle	GTEx
rs2069506	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs2069506	TSFM	cis	Muscle Skeletal	GTEx
rs2069506	METTL21B	cis	Esophagus Mucosa	GTEx
rs2069506	XRCC6BP1	cis	Thyroid	GTEx
rs2069506	TSFM	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58139400-58145400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:58139800-58144400	Weak transcription	Right Atrium	heart
3	chr12:58139800-58144600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:58139800-58144600	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:58139800-58144600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:58139800-58144600	Strong transcription	Fetal Muscle Leg	muscle
7	chr12:58139800-58144800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:58139800-58144800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:58139800-58144800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:58140000-58144000	Weak transcription	Fetal Brain Male	brain
11	chr12:58140000-58144200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:58140000-58144200	Strong transcription	Fetal Intestine Large	intestine
13	chr12:58140000-58144200	Strong transcription	Fetal Thymus	thymus
14	chr12:58140000-58144400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:58140000-58144400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:58140000-58144400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:58140000-58144400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:58140000-58144400	Weak transcription	Fetal Heart	heart
19	chr12:58140000-58144400	Strong transcription	Fetal Lung	lung
20	chr12:58140000-58144600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:58140000-58144600	Strong transcription	NHEK	skin
22	chr12:58140000-58144800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr12:58140000-58144800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:58140000-58144800	Weak transcription	Stomach Mucosa	stomach
25	chr12:58140200-58143200	Strong transcription	Brain Anterior Caudate	brain
26	chr12:58140200-58143400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:58140200-58143600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:58140200-58144200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:58140200-58144200	Strong transcription	Primary B cells from cord blood	blood
30	chr12:58140200-58144400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:58140200-58144400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:58140200-58144400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:58140200-58144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:58140200-58144400	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr12:58140200-58144400	Strong transcription	Fetal Brain Female	brain
36	chr12:58140200-58144400	Strong transcription	HMEC	breast
37	chr12:58140200-58144400	Strong transcription	NH-A	brain
38	chr12:58140200-58144400	Strong transcription	NHLF	lung
39	chr12:58140200-58144600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:58140200-58144600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:58140200-58144600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:58140200-58144600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:58140200-58144600	Strong transcription	Liver	Liver
44	chr12:58140200-58144600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr12:58140200-58144600	Strong transcription	Brain Substantia Nigra	brain
46	chr12:58140200-58144600	Strong transcription	Colon Smooth Muscle	Colon
47	chr12:58140200-58144600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:58140200-58144600	Strong transcription	Rectal Smooth Muscle	rectum
49	chr12:58140200-58144600	Strong transcription	HSMM	muscle
50	chr12:58140200-58144600	Strong transcription	Osteobl	bone

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