Variant report

Variant	rs12478265
Chromosome Location	chr2:20501496-20501497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20500817..20502817-chr2:20508534..20510980,2	K562	blood:
2	chr2:20500446..20501966-chr6:142366297..142367819,2	MCF-7	breast:
3	chr2:20494958..20496619-chr2:20499621..20501776,2	MCF-7	breast:
4	chr2:20496655..20499171-chr2:20500184..20502040,2	MCF-7	breast:
5	chr2:20497505..20499547-chr2:20501441..20503193,2	K562	blood:
6	chr2:20500446..20501946-chr3:73159867..73161430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223247	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10175853	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10187080	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10192042	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10206974	0.96[ASN][1000 genomes]
rs1043400	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10460445	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10460449	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10460450	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10460451	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10856797	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11096654	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11096659	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11888357	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895228	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896241	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898408	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11900127	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902769	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11903745	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465832	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12472685	0.88[ASN][1000 genomes]
rs12473500	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12474897	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13393733	0.88[ASN][1000 genomes]
rs17612703	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072464	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2080190	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2110410	0.80[EUR][1000 genomes]
rs2348703	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34678899	0.87[ASN][1000 genomes]
rs3796066	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821218	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62123442	0.88[ASN][1000 genomes]
rs6748274	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785217	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785218	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785278	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785282	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72785295	0.84[EUR][1000 genomes]
rs72785297	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785298	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785300	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785301	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72787406	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72787409	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72787411	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787415	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787433	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787499	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787500	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72787501	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72788905	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72788906	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs741188	0.82[EUR][1000 genomes]
rs7558385	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558833	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7563245	0.82[ASN][1000 genomes]
rs7579571	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7582642	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7595266	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9306890	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9306891	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][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	chr2:20460200-20528600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:20466000-20530400	Strong transcription	Fetal Thymus	thymus
3	chr2:20467000-20522400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:20467200-20526200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:20471800-20522600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:20471800-20533800	Strong transcription	Dnd41	blood
7	chr2:20474600-20528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:20475400-20522400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:20476200-20514400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:20476400-20521000	Strong transcription	Fetal Intestine Large	intestine
11	chr2:20476600-20516400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:20476600-20524800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:20476600-20526600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:20476800-20516800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr2:20478600-20516600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:20480400-20515400	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr2:20483200-20520200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:20483400-20505800	Weak transcription	Brain Substantia Nigra	brain
19	chr2:20483400-20514400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:20485000-20502600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:20486000-20502600	Weak transcription	Fetal Brain Male	brain
22	chr2:20488200-20516400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:20488400-20513200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:20488400-20516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:20488400-20517000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:20489200-20503000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:20489200-20505600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:20489200-20506200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:20489400-20513000	Weak transcription	Stomach Mucosa	stomach
30	chr2:20489400-20517400	Weak transcription	Psoas Muscle	Psoas
31	chr2:20489800-20525800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr2:20491000-20513400	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr2:20491400-20502600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:20491400-20504000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:20491400-20522600	Strong transcription	HepG2	liver
36	chr2:20491600-20513200	Weak transcription	Brain Angular Gyrus	brain
37	chr2:20491800-20513600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:20491800-20514800	Weak transcription	Gastric	stomach
39	chr2:20492000-20502600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:20492000-20505000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:20492000-20506800	Weak transcription	Right Atrium	heart
42	chr2:20492400-20505600	Weak transcription	Esophagus	oesophagus
43	chr2:20492400-20513200	Weak transcription	Aorta	Aorta
44	chr2:20492400-20525800	Strong transcription	Liver	Liver
45	chr2:20493600-20507200	Weak transcription	HMEC	breast
46	chr2:20494200-20502800	Weak transcription	Fetal Kidney	kidney
47	chr2:20494400-20502600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:20494400-20502600	Weak transcription	Pancreas	Pancrea
49	chr2:20494600-20505600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:20495400-20512200	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links