Variant report

Variant	rs17046959
Chromosome Location	chr2:55600321-55600322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55599888..55601639-chr2:55606569..55609062,2	K562	blood:

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10153861	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10181997	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10182704	0.86[AFR][1000 genomes]
rs10184362	1.00[EUR][1000 genomes]
rs10186158	1.00[EUR][1000 genomes]
rs10199332	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10201075	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10202943	1.00[EUR][1000 genomes]
rs10209908	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10518764	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11125565	0.86[AFR][1000 genomes]
rs11125566	0.86[AFR][1000 genomes]
rs12612806	0.81[AFR][1000 genomes]
rs12617891	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs13383527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13384739	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13389151	1.00[EUR][1000 genomes]
rs13389799	1.00[EUR][1000 genomes]
rs13390100	1.00[EUR][1000 genomes]
rs13394864	0.96[YRI][hapmap];1.00[AFR][1000 genomes]
rs13398447	1.00[EUR][1000 genomes]
rs13402277	0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13404740	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13405460	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13406929	1.00[EUR][1000 genomes]
rs13408706	1.00[EUR][1000 genomes]
rs13411077	1.00[EUR][1000 genomes]
rs13411257	1.00[EUR][1000 genomes]
rs13412682	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13416519	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13417988	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13419337	1.00[EUR][1000 genomes]
rs13424499	1.00[EUR][1000 genomes]
rs13426160	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13426766	1.00[EUR][1000 genomes]
rs13429863	1.00[EUR][1000 genomes]
rs1545554	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs17046801	1.00[EUR][1000 genomes]
rs17046820	1.00[EUR][1000 genomes]
rs17046828	1.00[EUR][1000 genomes]
rs17046829	1.00[EUR][1000 genomes]
rs17046835	1.00[EUR][1000 genomes]
rs17046837	1.00[EUR][1000 genomes]
rs17046881	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046896	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046898	1.00[EUR][1000 genomes]
rs17046954	0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046963	1.00[EUR][1000 genomes]
rs17046964	1.00[EUR][1000 genomes]
rs17264948	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902057	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs1902058	0.81[AFR][1000 genomes]
rs2043716	1.00[EUR][1000 genomes]
rs2045132	0.83[AFR][1000 genomes]
rs28434193	1.00[EUR][1000 genomes]
rs28498550	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2864831	0.84[YRI][hapmap];0.92[AFR][1000 genomes]
rs2864832	0.92[AFR][1000 genomes]
rs2867194	0.83[YRI][hapmap]
rs2902857	0.87[AFR][1000 genomes]
rs2920970	0.84[YRI][hapmap];0.92[AFR][1000 genomes]
rs2966466	0.84[YRI][hapmap];0.92[AFR][1000 genomes]
rs3099080	0.87[AFR][1000 genomes]
rs3099083	0.84[YRI][hapmap];0.91[AFR][1000 genomes]
rs3111408	0.85[AFR][1000 genomes]
rs3111409	0.85[AFR][1000 genomes]
rs3861571	0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3975804	0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4535081	0.80[AFR][1000 genomes]
rs4672037	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs56201519	1.00[EUR][1000 genomes]
rs57623398	1.00[EUR][1000 genomes]
rs59695161	1.00[EUR][1000 genomes]
rs60920006	1.00[EUR][1000 genomes]
rs6545485	1.00[EUR][1000 genomes]
rs6545486	1.00[EUR][1000 genomes]
rs6704701	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6707774	1.00[EUR][1000 genomes]
rs6710128	1.00[EUR][1000 genomes]
rs6714932	1.00[EUR][1000 genomes]
rs6715991	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6718909	0.86[AFR][1000 genomes]
rs6719677	1.00[EUR][1000 genomes]
rs6725968	0.84[YRI][hapmap];0.86[AFR][1000 genomes]
rs6726757	1.00[EUR][1000 genomes]
rs6729144	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6729490	0.94[AFR][1000 genomes]
rs6734415	1.00[EUR][1000 genomes]
rs6735009	1.00[EUR][1000 genomes]
rs6738517	1.00[EUR][1000 genomes]
rs6741630	1.00[EUR][1000 genomes]
rs6748541	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6754036	1.00[EUR][1000 genomes]
rs6758229	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6759625	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6759763	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6761771	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72918961	1.00[EUR][1000 genomes]
rs72918964	1.00[EUR][1000 genomes]
rs72918965	1.00[EUR][1000 genomes]
rs72918972	1.00[EUR][1000 genomes]
rs72918975	1.00[EUR][1000 genomes]
rs72923130	1.00[EUR][1000 genomes]
rs72923156	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72923157	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72923183	1.00[EUR][1000 genomes]
rs72923187	1.00[EUR][1000 genomes]
rs72923194	1.00[EUR][1000 genomes]
rs72923197	1.00[EUR][1000 genomes]
rs72924907	0.90[AFR][1000 genomes]
rs72924917	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72924922	1.00[EUR][1000 genomes]
rs72927340	1.00[EUR][1000 genomes]
rs72927384	1.00[EUR][1000 genomes]
rs72927388	1.00[EUR][1000 genomes]
rs72929306	1.00[EUR][1000 genomes]
rs7557555	0.85[AFR][1000 genomes]
rs7557956	0.81[AFR][1000 genomes]
rs7561604	1.00[EUR][1000 genomes]
rs7562535	1.00[EUR][1000 genomes]
rs7577510	1.00[EUR][1000 genomes]
rs7586440	0.86[AFR][1000 genomes]
rs7589558	1.00[EUR][1000 genomes]
rs7594907	1.00[EUR][1000 genomes]
rs7601588	0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs7606361	0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs9309264	0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
2	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:55537800-55609400	Weak transcription	Lung	lung
4	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
5	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:55564200-55605200	Weak transcription	Fetal Kidney	kidney
7	chr2:55572000-55610200	Weak transcription	Liver	Liver
8	chr2:55576000-55612200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:55579200-55602200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
11	chr2:55579400-55614400	Weak transcription	Fetal Brain Female	brain
12	chr2:55579400-55622400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
14	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55582200-55603600	Weak transcription	Ovary	ovary
17	chr2:55582800-55615000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:55583200-55605000	Weak transcription	HepG2	liver
19	chr2:55583400-55602000	Weak transcription	Left Ventricle	heart
20	chr2:55583400-55602400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:55583600-55606800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:55583600-55607200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:55584200-55612000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:55587400-55602000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
26	chr2:55589600-55628800	Weak transcription	Fetal Thymus	thymus
27	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:55590400-55622400	Weak transcription	GM12878-XiMat	blood
29	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:55592200-55617600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:55592200-55631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:55592800-55609400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:55592800-55609600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:55592800-55615600	Weak transcription	NHEK	skin
36	chr2:55592800-55617800	Weak transcription	A549	lung
37	chr2:55592800-55626600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
39	chr2:55593000-55622400	Weak transcription	Brain Angular Gyrus	brain
40	chr2:55593000-55622400	Weak transcription	Brain Anterior Caudate	brain
41	chr2:55593200-55611000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:55593400-55616400	Weak transcription	HUVEC	blood vessel
44	chr2:55593800-55631800	Weak transcription	Brain Germinal Matrix	brain
45	chr2:55594400-55603600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr2:55595400-55605000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:55596600-55603600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:55596600-55608400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:55597400-55601800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:55597800-55601200	Strong transcription	Dnd41	blood

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