Variant report

Variant	rs4951664
Chromosome Location	chr1:213364962-213364963
allele	A/T
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:31)

rs_ID	r²[population]
rs1045868	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10779599	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10864037	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10864039	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11120076	0.84[CEU][hapmap];0.91[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120102	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11120104	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12144379	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12401550	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1498355	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498356	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2359554	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3002284	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs34691780	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34868056	0.90[AMR][1000 genomes]
rs3738806	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3924768	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4393210	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951676	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60968477	0.89[AMR][1000 genomes]
rs6540777	0.85[AMR][1000 genomes]
rs6670496	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671019	0.87[AMR][1000 genomes]
rs6697921	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7517229	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7547782	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9645358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9728406	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4951664	ANGEL2	cis	Nerve Tibial	GTEx
rs4951664	ANGEL2	cis	Artery Tibial	GTEx
rs4951664	RPS6KC1	cis	Artery Tibial	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213301000-213371000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:213301000-213374800	Weak transcription	HSMM	muscle
3	chr1:213310000-213370400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:213326600-213422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:213328200-213387200	Weak transcription	Spleen	Spleen
6	chr1:213337800-213374400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:213340600-213424600	Weak transcription	Pancreas	Pancrea
8	chr1:213345600-213404600	Weak transcription	Osteobl	bone
9	chr1:213346200-213387400	Weak transcription	Gastric	stomach
10	chr1:213350400-213383200	Weak transcription	Placenta	Placenta
11	chr1:213357800-213387200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:213358000-213375000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:213360000-213371400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:213360200-213368000	Weak transcription	Right Ventricle	heart
15	chr1:213360400-213369600	Weak transcription	Liver	Liver
16	chr1:213360400-213371000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:213360400-213371000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:213360400-213371000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:213360400-213371200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:213360400-213373200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:213360400-213405200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:213360600-213367800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:213360600-213370400	Weak transcription	Primary B cells from cord blood	blood
24	chr1:213360600-213370800	Weak transcription	Fetal Lung	lung
25	chr1:213360600-213378000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:213360800-213372200	Weak transcription	Left Ventricle	heart
27	chr1:213361600-213386600	Weak transcription	Aorta	Aorta
28	chr1:213361800-213366400	Weak transcription	Ovary	ovary
29	chr1:213361800-213367400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:213361800-213367600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr1:213362000-213370400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:213362200-213415400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:213362800-213365200	Weak transcription	Fetal Stomach	stomach
34	chr1:213362800-213372400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:213363800-213368200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:213364200-213367600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:213364200-213370000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:213364400-213365800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:213364400-213371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:213364400-213372800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:213364600-213371000	Weak transcription	Adipose Nuclei	Adipose

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