Variant report

Variant	rs56092429
Chromosome Location	chr2:113428626-113428627
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	chr2:113423200..113424917-chr2:113426648..113428769,2	MCF-7	breast:
2	chr2:113422855..113425546-chr2:113428283..113429870,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10177499	0.81[EUR][1000 genomes]
rs10199279	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1061254	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10746527	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10779886	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11123144	0.84[EUR][1000 genomes]
rs13023311	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2312699	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35904547	0.82[EUR][1000 genomes]
rs3936697	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4630766	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4848286	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4849087	0.83[EUR][1000 genomes]
rs4849088	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849089	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849090	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849093	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4849094	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4849095	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4849096	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4849100	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61443276	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737094	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6747638	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6747928	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6751117	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6793	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72948491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7558138	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs885346	0.92[AMR][1000 genomes];0.85[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	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs56092429	AC079922.3	cis	Whole Blood	GTEx
rs56092429	AC079922.3	cis	Thyroid	GTEx
rs56092429	AC079922.3	cis	Muscle Skeletal	GTEx
rs56092429	AC079922.3	cis	Artery Aorta	GTEx
rs56092429	AC079922.3	cis	Artery Tibial	GTEx
rs56092429	AC079922.3	cis	Esophagus Muscularis	GTEx
rs56092429	AC079922.3	cis	lung	GTEx
rs56092429	AC079922.3	cis	Heart Left Ventricle	GTEx
rs56092429	AC079922.3	cis	Adipose Subcutaneous	GTEx
rs56092429	AC079922.3	cis	Nerve Tibial	GTEx
rs56092429	AC079922.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113419600-113431200	Weak transcription	Aorta	Aorta
2	chr2:113420800-113431200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:113421200-113431400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:113421400-113448400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:113421600-113429400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:113421600-113429400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:113421600-113438400	Weak transcription	Psoas Muscle	Psoas
8	chr2:113422200-113432000	Weak transcription	Left Ventricle	heart
9	chr2:113422600-113429400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:113422600-113431600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:113422600-113432000	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:113422800-113431400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:113422800-113437000	Weak transcription	HMEC	breast
14	chr2:113422800-113438200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:113423000-113429200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:113423000-113429800	Weak transcription	NHEK	skin
17	chr2:113423000-113430000	Weak transcription	NHDF-Ad	bronchial
18	chr2:113423000-113430800	Weak transcription	Fetal Brain Female	brain
19	chr2:113423200-113429200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:113423200-113429200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:113423200-113429400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:113423200-113429400	Weak transcription	Brain Germinal Matrix	brain
23	chr2:113423200-113431400	Weak transcription	Adipose Nuclei	Adipose
24	chr2:113423200-113431400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:113423200-113431400	Weak transcription	Spleen	Spleen
26	chr2:113423200-113432200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:113423200-113432200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:113423200-113432400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:113423200-113437000	Weak transcription	Lung	lung
30	chr2:113423200-113445000	Weak transcription	Fetal Brain Male	brain
31	chr2:113423400-113429200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:113423400-113429200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:113423400-113429400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:113423400-113430000	Weak transcription	Thymus	Thymus
35	chr2:113423400-113432000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:113423400-113437000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:113423400-113448400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:113423600-113429200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:113423600-113429200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr2:113423800-113431400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:113423800-113432000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:113424400-113432000	Weak transcription	Placenta	Placenta
43	chr2:113424600-113428800	Weak transcription	Primary T cells from cord blood	blood
44	chr2:113424800-113429200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:113424800-113431200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:113425400-113434200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:113426200-113430600	Enhancers	Liver	Liver
48	chr2:113427000-113429800	Enhancers	HUVEC	blood vessel
49	chr2:113428000-113428800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:113428000-113431200	Enhancers	Primary neutrophils fromperipheralblood	blood

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