Variant report

Variant	rs4393210
Chromosome Location	chr1:213373419-213373420
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10779599	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10864037	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10864039	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120076	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11120082	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11120084	0.85[AMR][1000 genomes]
rs11120100	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11120102	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120104	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144379	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12401550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1498355	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1498356	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2359554	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002284	0.86[CHB][hapmap];0.90[JPT][hapmap]
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]
rs3738806	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3924768	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4951664	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951676	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	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6671019	0.87[AMR][1000 genomes]
rs6697921	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7517229	0.92[ASN][1000 genomes]
rs7547782	0.86[ASN][1000 genomes]
rs9645358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9728406	0.92[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
rs4393210	RPS6KC1	cis	Artery Tibial	GTEx
rs4393210	ANGEL2	cis	Nerve Tibial	GTEx
rs4393210	ANGEL2	cis	Artery Tibial	GTEx

Chromatin state (count:71 , 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	chr1:213360400-213405200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:213360600-213378000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:213361600-213386600	Weak transcription	Aorta	Aorta
14	chr1:213362200-213415400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:213368200-213378200	Weak transcription	K562	blood
16	chr1:213368200-213386600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:213368200-213387200	Weak transcription	Lung	lung
18	chr1:213369600-213388800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:213369800-213398200	Weak transcription	Fetal Heart	heart
20	chr1:213370000-213374400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:213370600-213380200	Weak transcription	Fetal Stomach	stomach
22	chr1:213370800-213380600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:213370800-213427600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:213371000-213389400	Weak transcription	Right Ventricle	heart
25	chr1:213371400-213374600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:213371600-213374400	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr1:213371600-213385000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:213371600-213385400	Weak transcription	NHDF-Ad	bronchial
29	chr1:213371800-213374400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:213371800-213378000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:213371800-213386000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:213371800-213387200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:213371800-213388800	Weak transcription	HepG2	liver
34	chr1:213371800-213390000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:213372000-213389800	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:213372000-213393200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:213372000-213405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:213372600-213377400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:213372600-213390200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:213372600-213413800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:213372800-213374400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:213372800-213377800	Weak transcription	Fetal Kidney	kidney
43	chr1:213372800-213387200	Weak transcription	Liver	Liver
44	chr1:213372800-213414000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:213373000-213373800	Weak transcription	Primary T cells from cord blood	blood
46	chr1:213373000-213374000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:213373000-213374800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:213373000-213377200	Weak transcription	Ovary	ovary
49	chr1:213373000-213377400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:213373000-213378200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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