Variant report

Variant	rs62123451
Chromosome Location	chr2:20492554-20492555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20491737..20495195-chr2:20496209..20497993,3	K562	blood:
2	chr2:20422753..20425256-chr2:20490607..20493628,3	MCF-7	breast:
3	chr2:20484550..20486934-chr2:20490044..20492996,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10153828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10165087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10167509	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10168575	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10170538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10171861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10172088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10173098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10178561	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10179429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10182156	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10182228	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10182834	0.80[EUR][1000 genomes]
rs10184976	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10193751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10197941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10204489	0.80[EUR][1000 genomes]
rs10206963	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10207798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13390701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13391140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13398963	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13409830	0.80[EUR][1000 genomes]
rs13412971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13426989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56337814	0.89[AMR][1000 genomes]
rs60984167	0.89[AMR][1000 genomes]
rs62123441	0.80[EUR][1000 genomes]
rs62123443	0.80[EUR][1000 genomes]
rs62123444	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62123445	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62123446	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62123448	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62123450	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62123453	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62123454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62123455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62123458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62124599	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62124600	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62124601	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62124602	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62124603	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62124604	0.85[EUR][1000 genomes]
rs6715475	0.80[EUR][1000 genomes]
rs73214391	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73214393	0.93[EUR][1000 genomes]
rs73216207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73216223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73216230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73216236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73218112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73218129	0.89[AMR][1000 genomes]
rs73218135	0.89[AMR][1000 genomes]
rs7565347	0.93[EUR][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	nsv524207	chr2:20448561-20503436	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv999153	chr2:20467929-20521954	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1005366	chr2:20478859-20542134	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20454200-20499600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:20460200-20528600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:20465600-20500400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:20466000-20530400	Strong transcription	Fetal Thymus	thymus
5	chr2:20467000-20522400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:20467200-20526200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:20471800-20522600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:20471800-20533800	Strong transcription	Dnd41	blood
9	chr2:20474600-20528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:20475400-20522400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:20476200-20514400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:20476400-20492800	Strong transcription	GM12878-XiMat	blood
13	chr2:20476400-20500000	Strong transcription	Placenta	Placenta
14	chr2:20476400-20521000	Strong transcription	Fetal Intestine Large	intestine
15	chr2:20476600-20500600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:20476600-20516400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:20476600-20524800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:20476600-20526600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:20476800-20516800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:20478600-20516600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:20480400-20515400	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr2:20481800-20494800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:20482200-20496600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:20483000-20496400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:20483000-20496600	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:20483200-20498400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:20483200-20499000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:20483200-20520200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr2:20483400-20505800	Weak transcription	Brain Substantia Nigra	brain
30	chr2:20483400-20514400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr2:20484400-20494400	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:20485000-20502600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:20485400-20496600	Weak transcription	Fetal Brain Female	brain
34	chr2:20486000-20494600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:20486000-20502600	Weak transcription	Fetal Brain Male	brain
36	chr2:20486600-20500400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:20487400-20494600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:20487400-20494600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:20488000-20494400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:20488200-20516400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:20488400-20494800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:20488400-20513200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:20488400-20516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:20488400-20517000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:20488600-20494400	Strong transcription	Fetal Stomach	stomach
46	chr2:20488600-20494600	Strong transcription	Colonic Mucosa	Colon
47	chr2:20489200-20494000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:20489200-20496400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:20489200-20503000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:20489200-20505600	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links