Variant report

Variant	rs2589117
Chromosome Location	chr2:55528514-55528515
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	chr2:55528159..55530005-chr2:55532153..55533845,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10209598	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10496041	0.94[ASN][1000 genomes]
rs11125562	1.00[ASN][1000 genomes]
rs11125563	0.83[AFR][1000 genomes]
rs11884753	0.86[AFR][1000 genomes]
rs11892007	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11904107	1.00[ASN][1000 genomes]
rs12104902	1.00[ASN][1000 genomes]
rs12105322	1.00[ASN][1000 genomes]
rs12105731	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12617316	1.00[ASN][1000 genomes]
rs13016664	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031346	0.90[ASN][1000 genomes]
rs13407931	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1437387	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1437388	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1545120	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545121	0.87[AFR][1000 genomes]
rs17046834	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2249856	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289168	0.83[ASN][1000 genomes]
rs2576691	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576692	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576693	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576694	0.94[ASN][1000 genomes]
rs2576697	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2576698	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2576702	1.00[ASN][1000 genomes]
rs2589058	0.91[AFR][1000 genomes]
rs2589060	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589061	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589063	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589067	0.85[ASN][1000 genomes]
rs2589110	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589111	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589112	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589113	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589114	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589115	0.85[ASN][1000 genomes]
rs2589116	1.00[ASN][1000 genomes]
rs2917775	0.90[AFR][1000 genomes]
rs2917781	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920959	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920972	1.00[ASN][1000 genomes]
rs2920973	0.85[AFR][1000 genomes]
rs2966465	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57105158	1.00[ASN][1000 genomes]
rs59554860	0.94[ASN][1000 genomes]
rs6545484	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6705991	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6718747	1.00[ASN][1000 genomes]
rs6721211	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6726732	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6733567	1.00[ASN][1000 genomes]
rs6738970	0.83[AFR][1000 genomes]
rs6739348	0.83[AFR][1000 genomes]
rs6740631	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746287	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73939905	1.00[ASN][1000 genomes]
rs9784090	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	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
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
4	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
7	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
8	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
9	chr2:55510400-55529000	Weak transcription	Placenta	Placenta
10	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
11	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:55510600-55537400	Weak transcription	Lung	lung
13	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:55511000-55540600	Weak transcription	Spleen	Spleen
15	chr2:55511200-55542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
19	chr2:55512600-55546000	Weak transcription	Small Intestine	intestine
20	chr2:55513600-55531400	Strong transcription	Dnd41	blood
21	chr2:55514800-55549600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:55515800-55550400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:55518600-55532200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:55519400-55529400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:55519400-55533400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
28	chr2:55520000-55538800	Weak transcription	Ovary	ovary
29	chr2:55520000-55541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:55520200-55529000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:55520200-55531600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:55520200-55539000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:55521200-55529400	Strong transcription	Osteobl	bone
36	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:55521600-55529600	Strong transcription	HepG2	liver
38	chr2:55521800-55531600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:55522800-55529600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:55523000-55534800	Weak transcription	Primary T cells from cord blood	blood
41	chr2:55523000-55534800	Weak transcription	Liver	Liver
42	chr2:55523000-55537400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:55523000-55538800	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:55523000-55548000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
46	chr2:55523200-55537800	Weak transcription	HSMMtube	muscle
47	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:55523600-55528800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:55523600-55529000	Weak transcription	HMEC	breast
50	chr2:55523600-55529800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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