Variant report

Variant	rs2359554
Chromosome Location	chr1:213372832-213372833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10779599	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10864037	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10864039	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120084	0.85[AMR][1000 genomes]
rs11120100	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11120102	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120104	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144379	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12401550	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1498355	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1498356	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34691780	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34868056	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3924768	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4393210	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951664	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951676	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60968477	0.89[AMR][1000 genomes]
rs6540777	0.85[AMR][1000 genomes]
rs6670496	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6671019	0.87[AMR][1000 genomes]
rs7517229	0.92[ASN][1000 genomes]
rs7547782	0.86[ASN][1000 genomes]
rs9645358	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9728406	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392967	chr1:213271844-213490132	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv1794228	chr1:213355519-213379480	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1012014	chr1:213371127-213423214	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2359554	ANGEL2	cis	Artery Tibial	GTEx
rs2359554	ANGEL2	cis	Nerve Tibial	GTEx
rs2359554	RPS6KC1	cis	Artery Tibial	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213301000-213374800	Weak transcription	HSMM	muscle
2	chr1:213326600-213422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:213328200-213387200	Weak transcription	Spleen	Spleen
4	chr1:213337800-213374400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:213340600-213424600	Weak transcription	Pancreas	Pancrea
6	chr1:213345600-213404600	Weak transcription	Osteobl	bone
7	chr1:213346200-213387400	Weak transcription	Gastric	stomach
8	chr1:213350400-213383200	Weak transcription	Placenta	Placenta
9	chr1:213357800-213387200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:213358000-213375000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:213360400-213373200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:213360400-213405200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:213360600-213378000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:213361600-213386600	Weak transcription	Aorta	Aorta
15	chr1:213362200-213415400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:213368200-213378200	Weak transcription	K562	blood
17	chr1:213368200-213386600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:213368200-213387200	Weak transcription	Lung	lung
19	chr1:213369600-213388800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:213369800-213398200	Weak transcription	Fetal Heart	heart
21	chr1:213370000-213374400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:213370600-213380200	Weak transcription	Fetal Stomach	stomach
23	chr1:213370800-213380600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:213370800-213427600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:213371000-213373000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:213371000-213373000	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr1:213371000-213373200	ZNF genes & repeats	Primary B cells from cord blood	blood
28	chr1:213371000-213389400	Weak transcription	Right Ventricle	heart
29	chr1:213371400-213374600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:213371600-213373000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:213371600-213373000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:213371600-213373200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:213371600-213373200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:213371600-213373400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:213371600-213374400	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr1:213371600-213385000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:213371600-213385400	Weak transcription	NHDF-Ad	bronchial
38	chr1:213371800-213373000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:213371800-213373200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:213371800-213373400	Strong transcription	Adipose Nuclei	Adipose
41	chr1:213371800-213373400	Strong transcription	Fetal Lung	lung
42	chr1:213371800-213374400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:213371800-213378000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:213371800-213386000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:213371800-213387200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:213371800-213388800	Weak transcription	HepG2	liver
47	chr1:213371800-213390000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:213372000-213373000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:213372000-213373000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:213372000-213373200	Strong transcription	Primary hematopoietic stem cells	blood

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