Variant report

Variant	rs7558138
Chromosome Location	chr2:113419244-113419245
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113383706..113386562-chr2:113417388..113419756,2	MCF-7	breast:
2	chr2:113417080..113419534-chr2:113478132..113479929,2	K562	blood:
3	chr2:113418164..113419785-chr2:113446264..113447888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10177499	0.96[EUR][1000 genomes]
rs10199279	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1061254	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10746527	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10779886	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11123144	0.99[EUR][1000 genomes]
rs12994441	0.83[EUR][1000 genomes]
rs12996187	0.83[EUR][1000 genomes]
rs13023311	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17042199	0.82[EUR][1000 genomes]
rs2312699	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34109218	0.90[EUR][1000 genomes]
rs3936697	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4630766	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4848286	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4849087	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4849088	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4849089	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4849090	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4849092	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4849093	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4849094	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4849095	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4849096	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4849100	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56092429	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61443276	0.85[EUR][1000 genomes]
rs6542069	0.80[EUR][1000 genomes]
rs6737094	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6747638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6747928	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6751117	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6793	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72948491	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7559775	0.83[EUR][1000 genomes]
rs885346	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs7558138	AC079922.3	cis	Artery Tibial	GTEx
rs7558138	AC079922.3	cis	Heart Left Ventricle	GTEx
rs7558138	AC079922.3	cis	Muscle Skeletal	GTEx
rs7558138	AC079922.3	cis	Thyroid	GTEx
rs7558138	AC079922.3	cis	Artery Aorta	GTEx
rs7558138	AC079922.3	cis	Adipose Subcutaneous	GTEx
rs7558138	AC079922.3	cis	Whole Blood	GTEx
rs7558138	AC079922.3	cis	Esophagus Mucosa	GTEx
rs7558138	AC079922.3	cis	lung	GTEx
rs7558138	AC079922.3	cis	Esophagus Muscularis	GTEx
rs7558138	AC079922.3	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113405000-113423200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:113405200-113423200	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr2:113405200-113423800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr2:113405400-113422600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr2:113405400-113423200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:113405400-113423200	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:113405600-113422000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:113405800-113422600	Strong transcription	Fetal Muscle Leg	muscle
9	chr2:113406000-113419600	Strong transcription	Fetal Lung	lung
10	chr2:113406000-113423000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:113406200-113423400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:113406200-113423400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:113406200-113423600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:113406200-113424600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:113406400-113423000	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr2:113406400-113423000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:113406400-113423200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:113406800-113423200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:113407000-113420600	Strong transcription	Adipose Nuclei	Adipose
20	chr2:113407000-113423000	Strong transcription	NHDF-Ad	bronchial
21	chr2:113407000-113423200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:113407000-113423200	Strong transcription	Fetal Thymus	thymus
23	chr2:113407000-113423200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:113407000-113423400	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:113407000-113423400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:113407400-113419400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:113407400-113422800	Strong transcription	HSMMtube	muscle
28	chr2:113407600-113422200	Strong transcription	HSMM	muscle
29	chr2:113407600-113422600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:113407600-113422800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:113408200-113423000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:113408400-113422800	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:113408600-113421000	Strong transcription	Brain Anterior Caudate	brain
34	chr2:113408600-113422200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:113408800-113422600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:113409200-113423400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr2:113411200-113428200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:113411400-113423400	Strong transcription	Fetal Stomach	stomach
39	chr2:113412400-113420200	Strong transcription	Fetal Intestine Large	intestine
40	chr2:113412600-113421600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:113412600-113421600	Strong transcription	Pancreas	Pancrea
42	chr2:113412600-113423200	Strong transcription	Rectal Smooth Muscle	rectum
43	chr2:113412600-113423400	Strong transcription	Thymus	Thymus
44	chr2:113412800-113423400	Strong transcription	NHLF	lung
45	chr2:113413000-113420800	Strong transcription	Primary B cells from cord blood	blood
46	chr2:113413000-113421600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:113413400-113420200	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr2:113413800-113420400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:113414000-113422800	Strong transcription	Brain Cingulate Gyrus	brain
50	chr2:113414000-113423600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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