Variant report

Variant	rs11209599
Chromosome Location	chr1:70762310-70762311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10465863	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209600	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209602	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209603	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209608	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11209611	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11800138	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12028257	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12029977	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12030275	0.88[CEU][hapmap];0.89[AMR][1000 genomes]
rs12031053	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12034101	0.87[AMR][1000 genomes]
rs12036256	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12037272	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042565	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12565458	0.89[AMR][1000 genomes]
rs12565460	0.87[AMR][1000 genomes]
rs1327873	0.91[CEU][hapmap];0.89[AMR][1000 genomes]
rs17131276	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs17131285	0.83[CEU][hapmap];0.87[AMR][1000 genomes]
rs1969953	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4560989	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4650038	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4650041	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4650047	0.91[CEU][hapmap];0.89[AMR][1000 genomes]
rs56211824	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58696538	0.81[AFR][1000 genomes]
rs58997663	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59821213	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60602940	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61122312	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61587863	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61678482	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6686181	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72678630	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678644	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72678645	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72678646	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72680732	0.87[AMR][1000 genomes]
rs7539544	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs768433	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs998523	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014292	chr1:70689215-70799065	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	esv1792702	chr1:70755511-70818576	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11209599	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs11209599	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
2	chr1:70714000-70767000	Weak transcription	HSMMtube	muscle
3	chr1:70715600-70767800	Weak transcription	Small Intestine	intestine
4	chr1:70715800-70771000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:70716000-70775600	Weak transcription	Spleen	Spleen
6	chr1:70716200-70775200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:70716800-70769000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:70716800-70769400	Weak transcription	Right Ventricle	heart
9	chr1:70716800-70815800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:70717600-70765000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:70717600-70780400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:70717800-70765000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:70717800-70788200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:70719200-70783800	Weak transcription	A549	lung
15	chr1:70733800-70773400	Weak transcription	Fetal Kidney	kidney
16	chr1:70734000-70769600	Weak transcription	Pancreas	Pancrea
17	chr1:70734000-70786000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:70734400-70786000	Weak transcription	Psoas Muscle	Psoas
19	chr1:70734400-70813000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:70740600-70767000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:70744800-70768400	Weak transcription	Stomach Mucosa	stomach
22	chr1:70747000-70769400	Weak transcription	Fetal Heart	heart
23	chr1:70750000-70771800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:70752400-70767800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:70752800-70793400	Weak transcription	Gastric	stomach
26	chr1:70753600-70766600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:70753600-70767800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:70753600-70768800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:70753600-70769000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:70754200-70768800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:70754200-70780400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:70754400-70762400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:70754400-70762600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:70754400-70762600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:70754400-70767600	Strong transcription	Dnd41	blood
36	chr1:70754400-70767800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:70754600-70775400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:70755400-70762800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:70755400-70762800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:70755600-70762600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:70755600-70762800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:70755600-70767400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:70755600-70768800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:70755800-70762800	Strong transcription	Fetal Lung	lung
45	chr1:70755800-70775400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:70756600-70762600	Strong transcription	Hela-S3	cervix
47	chr1:70756600-70767000	Weak transcription	NHEK	skin
48	chr1:70756800-70764600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:70757000-70769200	Weak transcription	Colonic Mucosa	Colon
50	chr1:70757000-70799800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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