Variant report

Variant	rs17569145
Chromosome Location	chr1:225830735-225830736
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10429871	0.93[EUR][1000 genomes]
rs11801322	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12027872	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12039453	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1340868	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537877	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537878	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845078	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500089	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17500562	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500604	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500639	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500679	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500814	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17500944	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17501138	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501208	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501249	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501775	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501845	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501956	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502068	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502075	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502297	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502774	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502823	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17502858	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502961	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503792	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17559267	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17559587	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17560021	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17560215	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17560579	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561095	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561221	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561228	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561368	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561451	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561781	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17562010	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17562052	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17568665	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17569049	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17569194	1.00[ASN][1000 genomes]
rs1832229	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876085	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876086	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617210	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3947140	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687755	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73125707	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs954615	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225809800-225837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:225813600-225837600	Weak transcription	HUVEC	blood vessel
3	chr1:225813800-225838600	Weak transcription	HMEC	breast
4	chr1:225814600-225835800	Weak transcription	HSMMtube	muscle
5	chr1:225815800-225839000	Weak transcription	Fetal Intestine Large	intestine
6	chr1:225816000-225832400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:225816000-225834200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:225816000-225838400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:225816000-225838600	Weak transcription	Fetal Kidney	kidney
10	chr1:225816200-225835400	Weak transcription	Fetal Heart	heart
11	chr1:225816200-225836000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:225816200-225836600	Weak transcription	Adipose Nuclei	Adipose
13	chr1:225816800-225832000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:225817200-225834000	Weak transcription	Psoas Muscle	Psoas
15	chr1:225819000-225831000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:225819000-225832200	Weak transcription	NHDF-Ad	bronchial
17	chr1:225819600-225836400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:225820000-225835800	Weak transcription	Brain Anterior Caudate	brain
19	chr1:225820800-225837200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:225823400-225830800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:225823600-225834200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:225823800-225835400	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:225823800-225836600	Weak transcription	NHLF	lung
24	chr1:225824000-225832200	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:225824200-225834400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:225825000-225837400	Weak transcription	Hela-S3	cervix
27	chr1:225825600-225831600	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:225825600-225839600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:225825800-225837200	Weak transcription	NHEK	skin
30	chr1:225826200-225838800	Weak transcription	Fetal Intestine Small	intestine
31	chr1:225826200-225839400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:225826600-225831000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:225826800-225833600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:225827000-225831600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:225827400-225834000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:225827600-225832800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:225827800-225832400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:225827800-225836000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:225828200-225832400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:225828200-225832600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:225828200-225833400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:225828200-225835400	Weak transcription	HepG2	liver
43	chr1:225828400-225831600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:225828400-225832800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:225828600-225832800	Weak transcription	Brain Germinal Matrix	brain
46	chr1:225828600-225836200	Weak transcription	Right Atrium	heart
47	chr1:225828800-225831600	Strong transcription	Fetal Stomach	stomach
48	chr1:225828800-225833200	Strong transcription	Fetal Lung	lung
49	chr1:225829400-225830800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:225829600-225831400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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