Variant report

Variant	rs2589112
Chromosome Location	chr2:55519798-55519799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55516061..55518491-chr2:55518529..55520349,2	K562	blood:
2	chr2:55514301..55516151-chr2:55518959..55520928,3	MCF-7	breast:
3	chr2:55494684..55499569-chr2:55516943..55523168,5	K562	blood:
4	chr2:55513717..55517670-chr2:55518024..55521740,6	K562	blood:
5	chr2:55518930..55520910-chr2:55525941..55528054,2	K562	blood:
6	chr2:55516323..55518543-chr2:55519705..55522425,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10209598	0.94[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	0.90[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	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12617316	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13016664	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031346	0.90[ASN][1000 genomes]
rs13407931	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1437387	0.96[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	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545121	0.83[AFR][1000 genomes]
rs17046834	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2249856	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289168	0.83[ASN][1000 genomes]
rs2576691	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576692	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576693	0.84[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	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2576702	1.00[ASN][1000 genomes]
rs2589058	0.95[AFR][1000 genomes]
rs2589060	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589061	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589063	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589067	0.85[ASN][1000 genomes]
rs2589110	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589111	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589113	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589114	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589115	0.85[ASN][1000 genomes]
rs2589116	1.00[ASN][1000 genomes]
rs2589117	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917775	0.89[AFR][1000 genomes]
rs2917781	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920959	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920972	1.00[ASN][1000 genomes]
rs2920973	0.84[AFR][1000 genomes]
rs2966465	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57105158	1.00[ASN][1000 genomes]
rs59554860	0.94[ASN][1000 genomes]
rs6545484	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6705991	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6718747	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721211	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6726732	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6733567	1.00[ASN][1000 genomes]
rs6738970	0.87[AFR][1000 genomes]
rs6739348	0.87[AFR][1000 genomes]
rs6740631	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746287	0.84[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:8 , 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	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:118 , 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	chr2:55509800-55521800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:55510000-55521600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:55510000-55521600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:55510000-55521800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:55510000-55521800	Weak transcription	Fetal Brain Male	brain
9	chr2:55510000-55521800	Weak transcription	NHEK	skin
10	chr2:55510000-55522000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:55510000-55522200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:55510000-55522200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:55510000-55522400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:55510000-55522400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:55510000-55522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
17	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:55510200-55520600	Weak transcription	HSMMtube	muscle
20	chr2:55510200-55521800	Weak transcription	Fetal Kidney	kidney
21	chr2:55510200-55522200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:55510200-55522400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:55510200-55522400	Weak transcription	NHLF	lung
24	chr2:55510200-55522600	Weak transcription	Aorta	Aorta
25	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
26	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
27	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
28	chr2:55510400-55522400	Weak transcription	Left Ventricle	heart
29	chr2:55510400-55529000	Weak transcription	Placenta	Placenta
30	chr2:55510600-55521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:55510600-55522400	Weak transcription	A549	lung
32	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
33	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:55510600-55537400	Weak transcription	Lung	lung
35	chr2:55510800-55521200	Weak transcription	Osteobl	bone
36	chr2:55510800-55521800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:55511000-55521600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:55511000-55521800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:55511000-55521800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:55511000-55540600	Weak transcription	Spleen	Spleen
42	chr2:55511200-55521800	Weak transcription	Liver	Liver
43	chr2:55511200-55521800	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:55511200-55521800	Weak transcription	Thymus	Thymus
45	chr2:55511200-55522200	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:55511200-55542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr2:55511400-55521800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:55511400-55522200	Weak transcription	Primary T cells from cord blood	blood
50	chr2:55511600-55521800	Weak transcription	K562	blood

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