Variant report

Variant	rs6419470
Chromosome Location	chr1:213389483-213389484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10127851	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10864034	0.83[AMR][1000 genomes]
rs10864036	0.82[AMR][1000 genomes]
rs10864038	0.93[AMR][1000 genomes]
rs1391549	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1391550	0.92[AMR][1000 genomes]
rs1498357	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1566247	0.83[AMR][1000 genomes]
rs17020338	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1995151	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2173398	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2494767	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2647387	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2817976	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2817978	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2817981	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2841425	0.82[ASN][1000 genomes]
rs2841427	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2841439	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4655386	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4951479	0.82[AMR][1000 genomes]
rs4951677	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6419469	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6540778	0.82[AMR][1000 genomes]
rs6540780	0.85[AMR][1000 genomes]
rs6540781	0.90[AMR][1000 genomes]
rs6540782	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6657234	0.90[AMR][1000 genomes]
rs6658259	0.81[AMR][1000 genomes]
rs6666814	0.82[AMR][1000 genomes]
rs6671872	0.90[AMR][1000 genomes]
rs6691488	0.83[AMR][1000 genomes]
rs6692056	0.85[AMR][1000 genomes]
rs6692144	0.83[AMR][1000 genomes]
rs6693291	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6700169	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7535369	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7547274	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9308430	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429901	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429902	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9430118	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9430120	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9430121	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9430122	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9430123	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv275574	chr1:213382672-213393600	Strong transcription Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
4	nsv1001201	chr1:213385827-213428021	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6419470	RPS6KC1	cis	Artery Tibial	GTEx
rs6419470	ANGEL2	cis	Nerve Tibial	GTEx

Chromatin state (count:74 , 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	chr1:213340600-213424600	Weak transcription	Pancreas	Pancrea
3	chr1:213345600-213404600	Weak transcription	Osteobl	bone
4	chr1:213360400-213405200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:213362200-213415400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:213369800-213398200	Weak transcription	Fetal Heart	heart
7	chr1:213370800-213427600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:213371800-213390000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:213372000-213389800	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:213372000-213393200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:213372000-213405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:213372600-213390200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:213372600-213413800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:213372800-213414000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:213373000-213398000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:213373000-213405200	Weak transcription	Left Ventricle	heart
17	chr1:213373000-213414200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:213373000-213423000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:213373200-213405000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:213373200-213417000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:213375200-213390400	Weak transcription	HSMMtube	muscle
22	chr1:213375800-213405200	Weak transcription	Psoas Muscle	Psoas
23	chr1:213375800-213405200	Weak transcription	HSMM	muscle
24	chr1:213376400-213390600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:213376800-213391800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:213376800-213414200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:213377800-213389800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:213378800-213405200	Weak transcription	K562	blood
29	chr1:213378800-213421200	Weak transcription	Fetal Kidney	kidney
30	chr1:213379000-213405200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:213381600-213425000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:213382600-213405000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:213385600-213407000	Weak transcription	Stomach Mucosa	stomach
34	chr1:213386000-213405400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:213386600-213404800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:213387400-213391400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:213387400-213398400	Weak transcription	Primary T cells from cord blood	blood
38	chr1:213387400-213414000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:213387600-213405000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:213388000-213405200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:213388000-213405200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:213388000-213414400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:213388000-213424600	Weak transcription	Gastric	stomach
44	chr1:213388200-213390200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:213388200-213390200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:213388200-213390200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:213388200-213392400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:213388200-213414000	Weak transcription	Aorta	Aorta
49	chr1:213388200-213414000	Weak transcription	Liver	Liver
50	chr1:213388200-213414200	Weak transcription	Ovary	ovary

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