Variant report

Variant	rs6658259
Chromosome Location	chr1:213282565-213282566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10127851	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10465694	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10864034	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10864036	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10864038	0.85[AMR][1000 genomes]
rs1391549	0.83[AMR][1000 genomes]
rs1391550	0.84[AMR][1000 genomes]
rs1498357	0.84[AMR][1000 genomes]
rs1566247	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1566248	0.82[EUR][1000 genomes]
rs1976333	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1995151	0.84[AMR][1000 genomes]
rs2173398	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2494767	0.82[AMR][1000 genomes]
rs2647387	0.84[AMR][1000 genomes]
rs2817976	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2817978	0.84[AMR][1000 genomes]
rs2817981	0.84[AMR][1000 genomes]
rs2841427	0.83[AMR][1000 genomes]
rs2841439	0.84[AMR][1000 genomes]
rs2935219	0.83[AMR][1000 genomes]
rs2936011	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3010779	0.81[AMR][1000 genomes]
rs3010789	0.81[AMR][1000 genomes]
rs4543872	0.81[AMR][1000 genomes]
rs4951476	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4951478	0.81[EUR][1000 genomes]
rs4951479	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4951662	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4951677	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6419470	0.81[AMR][1000 genomes]
rs6540774	0.81[EUR][1000 genomes]
rs6540776	0.82[EUR][1000 genomes]
rs6540778	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6540780	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6540781	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6540782	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6657234	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6666814	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670025	0.83[ASN][1000 genomes]
rs6671872	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6679510	0.89[EUR][1000 genomes]
rs6691488	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6692056	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6692144	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6693291	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6699158	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6700169	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7535369	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7547274	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9308430	0.81[AMR][1000 genomes]
rs9430118	0.81[AMR][1000 genomes]
rs9430123	0.82[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6658259	RPS6KC1	cis	Artery Tibial	GTEx
rs6658259	ANGEL2	cis	Nerve Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213229400-213283400	Weak transcription	Hela-S3	cervix
2	chr1:213244200-213296200	Weak transcription	NHDF-Ad	bronchial
3	chr1:213246800-213283800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:213251200-213293000	Weak transcription	NH-A	brain
5	chr1:213252600-213297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:213254800-213297400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:213256800-213284000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:213258800-213284200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:213259800-213284000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:213261400-213284000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:213261600-213283800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:213261600-213283800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:213261600-213283800	Weak transcription	HSMMtube	muscle
14	chr1:213261600-213284000	Weak transcription	Pancreas	Pancrea
15	chr1:213261600-213284000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:213261600-213293000	Weak transcription	NHLF	lung
17	chr1:213261600-213296000	Weak transcription	Lung	lung
18	chr1:213261600-213309200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:213261600-213327400	Weak transcription	Aorta	Aorta
20	chr1:213261800-213284000	Weak transcription	Left Ventricle	heart
21	chr1:213261800-213285200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:213262200-213284400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:213262600-213284400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:213263200-213284000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:213268400-213284400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:213268600-213284400	Weak transcription	Brain Angular Gyrus	brain
27	chr1:213269200-213293000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:213269200-213296200	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:213269400-213284000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:213269400-213308400	Weak transcription	Ovary	ovary
31	chr1:213269600-213311800	Weak transcription	Primary B cells from cord blood	blood
32	chr1:213269800-213284000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:213269800-213284000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:213269800-213285800	Weak transcription	Dnd41	blood
35	chr1:213270000-213296000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:213271000-213284200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:213271000-213297000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:213271200-213296200	Weak transcription	Fetal Intestine Small	intestine
39	chr1:213271200-213309200	Weak transcription	Adipose Nuclei	Adipose
40	chr1:213271400-213296400	Weak transcription	Fetal Intestine Large	intestine
41	chr1:213271600-213284000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:213271600-213310200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:213273200-213284200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:213273200-213286600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:213280400-213284000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:213280800-213297400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:213281000-213293000	Weak transcription	HSMM	muscle
48	chr1:213281200-213283800	Weak transcription	Stomach Mucosa	stomach
49	chr1:213281200-213284000	Weak transcription	A549	lung
50	chr1:213281200-213285400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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