Variant report

Variant	rs12090117
Chromosome Location	chr1:57153956-57153957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11206874	1.00[AMR][1000 genomes]
rs11206876	1.00[AMR][1000 genomes]
rs11206904	1.00[AMR][1000 genomes]
rs12060663	1.00[AMR][1000 genomes]
rs12081693	1.00[AMR][1000 genomes]
rs12089982	1.00[AMR][1000 genomes]
rs12094381	1.00[AMR][1000 genomes]
rs12095026	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13376460	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2897036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3991779	1.00[AMR][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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv523032	chr1:57116909-57249558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	esv1831276	chr1:57139370-57175158	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	nsv520726	chr1:57143986-57205666	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57122800-57169600	Weak transcription	Ovary	ovary
2	chr1:57125600-57169800	Weak transcription	Aorta	Aorta
3	chr1:57135400-57160200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:57136200-57161400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:57144200-57165000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:57144200-57171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:57144400-57169400	Weak transcription	Fetal Kidney	kidney
8	chr1:57144400-57173600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:57149600-57166000	Weak transcription	Right Ventricle	heart
10	chr1:57150000-57165800	Weak transcription	Left Ventricle	heart
11	chr1:57150600-57168000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:57151000-57165600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:57151400-57165400	Weak transcription	Fetal Heart	heart
14	chr1:57152400-57154000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:57152400-57154000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:57152400-57154000	Weak transcription	NHDF-Ad	bronchial
17	chr1:57152400-57154200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:57152400-57154200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:57152400-57154200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:57152400-57165800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:57153000-57154800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:57153200-57154200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr1:57153200-57154800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:57153400-57154600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr1:57153400-57155000	Enhancers	HepG2	liver
26	chr1:57153600-57154000	Flanking Active TSS	A549	lung
27	chr1:57153600-57154600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr1:57153600-57154600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:57153600-57154600	Enhancers	HUVEC	blood vessel
30	chr1:57153600-57154800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr1:57153600-57155000	Enhancers	Hela-S3	cervix
32	chr1:57153600-57155000	Enhancers	HMEC	breast
33	chr1:57153600-57155000	Enhancers	NH-A	brain
34	chr1:57153600-57155000	Enhancers	NHEK	skin
35	chr1:57153800-57154200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:57153800-57154400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:57153800-57154600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:57153800-57154600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr1:57153800-57154800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:57153800-57154800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:57153800-57155000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:57153800-57155000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:57153800-57155000	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr1:57153800-57155000	Enhancers	Osteobl	bone

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