Variant report

Variant	rs17500089
Chromosome Location	chr1:225649539-225649540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225626720..225628379-chr1:225647904..225650755,2	K562	blood:
2	chr1:225648477..225651119-chr1:225966156..225969061,2	K562	blood:
3	chr1:225637801..225642696-chr1:225647950..225650939,4	K562	blood:
4	chr1:225646346..225648004-chr1:225649524..225651043,2	K562	blood:
5	chr1:225646305..225648757-chr1:225649524..225652760,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11801322	0.81[ASN][1000 genomes]
rs1340868	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1537877	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1537878	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16845078	0.81[ASN][1000 genomes]
rs17500562	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500604	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500639	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500679	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500814	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500944	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501138	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501208	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501249	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501775	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501845	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501956	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502068	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502075	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502297	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502774	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502823	0.87[AMR][1000 genomes]
rs17502858	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17502961	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17503792	0.90[ASN][1000 genomes]
rs17558869	0.90[ASN][1000 genomes]
rs17559267	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17559587	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17560021	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17560215	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17560579	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561095	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561221	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561228	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561368	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561451	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561781	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17562010	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17562052	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17568665	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17569049	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17569145	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17569194	0.90[ASN][1000 genomes]
rs1832229	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876085	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876086	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28617210	0.81[ASN][1000 genomes]
rs3947140	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6679804	0.90[ASN][1000 genomes]
rs6687755	0.81[ASN][1000 genomes]
rs73125707	0.81[ASN][1000 genomes]
rs954615	0.87[AMR][1000 genomes];0.90[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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225636200-225650000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:225642400-225650800	Weak transcription	Right Atrium	heart
3	chr1:225642400-225653000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
5	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:225642800-225650000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:225642800-225652800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:225643000-225650400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:225643000-225651000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:225646400-225653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:225647000-225651600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:225647000-225651600	Enhancers	Fetal Muscle Leg	muscle
13	chr1:225647000-225653600	Enhancers	Esophagus	oesophagus
14	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
15	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:225647200-225649600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:225647200-225649800	Enhancers	Thymus	Thymus
18	chr1:225647200-225651600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:225647400-225651200	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:225647600-225649600	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:225647600-225650200	Enhancers	Spleen	Spleen
23	chr1:225647600-225650200	Enhancers	A549	lung
24	chr1:225647600-225652000	Enhancers	Fetal Stomach	stomach
25	chr1:225647600-225653800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:225647800-225649600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:225647800-225649600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:225647800-225649800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:225647800-225649800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr1:225647800-225650200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:225647800-225653400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:225648000-225649600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr1:225648000-225649600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr1:225648000-225649800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:225648000-225650200	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr1:225648000-225651400	Enhancers	Fetal Brain Male	brain
37	chr1:225648000-225652600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:225648200-225649800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:225648200-225651000	Weak transcription	Fetal Intestine Small	intestine
40	chr1:225648400-225649800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:225648400-225650200	Enhancers	Brain Germinal Matrix	brain
42	chr1:225648400-225653400	Weak transcription	Fetal Intestine Large	intestine
43	chr1:225648600-225650800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:225648600-225651000	Weak transcription	Gastric	stomach
45	chr1:225648600-225651200	Enhancers	Fetal Brain Female	brain
46	chr1:225648600-225652800	Weak transcription	Fetal Kidney	kidney
47	chr1:225648800-225649600	Enhancers	H1 Cell Line	embryonic stem cell
48	chr1:225648800-225649600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:225648800-225649800	Enhancers	Pancreas	Pancrea
50	chr1:225648800-225650000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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