Variant report

Variant	rs11120104
Chromosome Location	chr1:213381172-213381173
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10779599	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10864037	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10864039	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120084	0.83[AMR][1000 genomes]
rs11120100	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120102	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144379	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12401550	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1498355	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1498356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359554	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34691780	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34868056	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3924768	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4393210	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951664	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4951676	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60968477	0.87[AMR][1000 genomes]
rs6540777	0.83[AMR][1000 genomes]
rs6670496	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671019	0.85[AMR][1000 genomes]
rs7517229	0.88[ASN][1000 genomes]
rs7547782	0.85[ASN][1000 genomes]
rs9645358	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9728406	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	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
3	nsv826598	chr1:213378117-213387293	Weak transcription Enhancers ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11120104	RPS6KC1	cis	Artery Tibial	GTEx
rs11120104	ANGEL2	cis	Nerve Tibial	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213326600-213422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:213328200-213387200	Weak transcription	Spleen	Spleen
3	chr1:213340600-213424600	Weak transcription	Pancreas	Pancrea
4	chr1:213345600-213404600	Weak transcription	Osteobl	bone
5	chr1:213346200-213387400	Weak transcription	Gastric	stomach
6	chr1:213350400-213383200	Weak transcription	Placenta	Placenta
7	chr1:213357800-213387200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:213360400-213405200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:213361600-213386600	Weak transcription	Aorta	Aorta
10	chr1:213362200-213415400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:213368200-213386600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:213368200-213387200	Weak transcription	Lung	lung
13	chr1:213369600-213388800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:213369800-213398200	Weak transcription	Fetal Heart	heart
15	chr1:213370800-213427600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:213371000-213389400	Weak transcription	Right Ventricle	heart
17	chr1:213371600-213385000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:213371600-213385400	Weak transcription	NHDF-Ad	bronchial
19	chr1:213371800-213386000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:213371800-213387200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:213371800-213388800	Weak transcription	HepG2	liver
22	chr1:213371800-213390000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:213372000-213389800	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:213372000-213393200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:213372000-213405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:213372600-213390200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:213372600-213413800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:213372800-213387200	Weak transcription	Liver	Liver
29	chr1:213372800-213414000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:213373000-213385200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:213373000-213386000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:213373000-213398000	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:213373000-213405200	Weak transcription	Left Ventricle	heart
34	chr1:213373000-213414200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:213373000-213423000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:213373200-213381800	Weak transcription	Brain Germinal Matrix	brain
37	chr1:213373200-213385600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:213373200-213386600	Weak transcription	Dnd41	blood
39	chr1:213373200-213405000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:213373200-213417000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:213374200-213385600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:213374400-213385200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:213374400-213385600	Weak transcription	Fetal Brain Female	brain
44	chr1:213374400-213386600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:213375200-213390400	Weak transcription	HSMMtube	muscle
46	chr1:213375400-213388600	Weak transcription	HMEC	breast
47	chr1:213375800-213405200	Weak transcription	Psoas Muscle	Psoas
48	chr1:213375800-213405200	Weak transcription	HSMM	muscle
49	chr1:213376000-213387200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:213376000-213387200	Weak transcription	Esophagus	oesophagus

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