Variant report

Variant	rs2589110
Chromosome Location	chr2:55522422-55522423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55521570..55523251-chr2:55525570..55527092,2	MCF-7	breast:
2	chr2:55517623..55519304-chr2:55522229..55524562,2	K562	blood:
3	chr2:55494684..55499569-chr2:55516943..55523168,5	K562	blood:
4	chr2:55520326..55522931-chr2:55543015..55545040,2	K562	blood:
5	chr2:55516323..55518543-chr2:55519705..55522425,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10209598	1.00[ASN][1000 genomes]
rs10496041	0.94[ASN][1000 genomes]
rs11125562	1.00[ASN][1000 genomes]
rs11892007	1.00[ASN][1000 genomes]
rs11904107	1.00[ASN][1000 genomes]
rs12104902	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12105322	1.00[ASN][1000 genomes]
rs12105731	1.00[ASN][1000 genomes]
rs12617316	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13016664	1.00[ASN][1000 genomes]
rs13031346	0.90[ASN][1000 genomes]
rs13407931	1.00[ASN][1000 genomes]
rs1437387	1.00[ASN][1000 genomes]
rs1437388	1.00[ASN][1000 genomes]
rs1545120	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046834	0.94[ASN][1000 genomes]
rs2249856	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289168	0.83[ASN][1000 genomes]
rs2576691	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576692	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576694	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576697	1.00[ASN][1000 genomes]
rs2576698	1.00[ASN][1000 genomes]
rs2576702	1.00[ASN][1000 genomes]
rs2589060	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589061	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589063	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589067	0.85[ASN][1000 genomes]
rs2589111	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589112	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589113	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589114	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589115	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2589116	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589117	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917781	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920959	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920972	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2966465	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57105158	1.00[ASN][1000 genomes]
rs59554860	0.94[ASN][1000 genomes]
rs6545484	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6705991	1.00[ASN][1000 genomes]
rs6718747	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721211	1.00[ASN][1000 genomes]
rs6726732	1.00[ASN][1000 genomes]
rs6733567	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6740631	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746287	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:115 , 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	chr2:55509600-55522600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55510000-55522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
6	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:55510200-55522600	Weak transcription	Aorta	Aorta
9	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
10	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
11	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
12	chr2:55510400-55529000	Weak transcription	Placenta	Placenta
13	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
14	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:55510600-55537400	Weak transcription	Lung	lung
16	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:55511000-55540600	Weak transcription	Spleen	Spleen
18	chr2:55511200-55542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
22	chr2:55512600-55525000	Weak transcription	Gastric	stomach
23	chr2:55512600-55546000	Weak transcription	Small Intestine	intestine
24	chr2:55513200-55525400	Strong transcription	Fetal Thymus	thymus
25	chr2:55513600-55531400	Strong transcription	Dnd41	blood
26	chr2:55514200-55522600	Weak transcription	Fetal Stomach	stomach
27	chr2:55514800-55549600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:55515800-55550400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:55516200-55525400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:55516400-55527800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:55518000-55524200	Strong transcription	HSMM	muscle
32	chr2:55518600-55532200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:55519400-55524400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:55519400-55529400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:55519400-55533400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:55519600-55524000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:55519800-55523800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
40	chr2:55520000-55523200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr2:55520000-55523200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:55520000-55523800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr2:55520000-55538800	Weak transcription	Ovary	ovary
44	chr2:55520000-55541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:55520200-55529000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:55520200-55531600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:55520200-55539000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr2:55520600-55523200	Active TSS	HSMMtube	muscle

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