Variant report

Variant	rs10864039
Chromosome Location	chr1:213449418-213449419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213433608..213435913-chr1:213449399..213451147,2	K562	blood:
2	chr1:213445277..213447127-chr1:213447433..213449979,2	K562	blood:
3	chr1:213447316..213454346-chr1:213454663..213460102,7	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10779599	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10864037	0.88[AMR][1000 genomes]
rs11120100	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11120102	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11120104	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12144379	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12401550	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1498355	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1498356	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2359554	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34691780	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34868056	0.85[AMR][1000 genomes]
rs3924768	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4393210	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951664	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4951676	0.90[AMR][1000 genomes]
rs60968477	0.81[AMR][1000 genomes]
rs6670496	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7517229	0.81[ASN][1000 genomes]
rs9645358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9728406	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10864039	RPS6KC1	cis	Artery Tibial	GTEx
rs10864039	ANGEL2	cis	Nerve Tibial	GTEx
rs10864039	ANGEL2	cis	parietal	SCAN
rs10864039	ANGEL2	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213388200-213455400	Weak transcription	Placenta	Placenta
2	chr1:213402800-213454800	Weak transcription	Brain Substantia Nigra	brain
3	chr1:213405600-213454800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:213405800-213457600	Weak transcription	NHLF	lung
5	chr1:213406000-213450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:213406200-213454800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:213412600-213452400	Weak transcription	Right Ventricle	heart
8	chr1:213415400-213450200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:213415600-213451000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:213415600-213453800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:213417200-213453600	Weak transcription	HSMMtube	muscle
12	chr1:213427000-213451400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:213431200-213450600	Weak transcription	Psoas Muscle	Psoas
14	chr1:213433800-213454800	Weak transcription	Brain Anterior Caudate	brain
15	chr1:213434400-213454800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:213434400-213454800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:213434600-213453800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:213434600-213453800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:213435200-213456200	Weak transcription	Esophagus	oesophagus
20	chr1:213438600-213449600	Weak transcription	Gastric	stomach
21	chr1:213440000-213451400	Weak transcription	NH-A	brain
22	chr1:213440000-213469800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:213440400-213450800	Weak transcription	Fetal Stomach	stomach
24	chr1:213440600-213449800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:213440600-213452400	Weak transcription	Aorta	Aorta
26	chr1:213440600-213454200	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:213440600-213454400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:213440600-213454800	Weak transcription	Left Ventricle	heart
29	chr1:213440800-213449800	Weak transcription	GM12878-XiMat	blood
30	chr1:213440800-213450800	Weak transcription	Fetal Intestine Small	intestine
31	chr1:213440800-213451000	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:213440800-213457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:213440800-213465800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:213441000-213454600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:213443600-213452200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:213443600-213457000	Weak transcription	Lung	lung
37	chr1:213444000-213454800	Weak transcription	Fetal Brain Female	brain
38	chr1:213444000-213455000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:213444200-213457600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:213445400-213450000	Strong transcription	Adipose Nuclei	Adipose
41	chr1:213445600-213454400	Weak transcription	Brain Germinal Matrix	brain
42	chr1:213445800-213449600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:213447200-213454400	Enhancers	HepG2	liver
44	chr1:213447400-213457600	Weak transcription	NHDF-Ad	bronchial
45	chr1:213447800-213450200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:213447800-213450200	Weak transcription	HUVEC	blood vessel
47	chr1:213447800-213451200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:213447800-213452200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:213447800-213454400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:213447800-213454600	Weak transcription	Brain Hippocampus Middle	brain

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