Variant report

Variant	rs72787433
Chromosome Location	chr2:20513364-20513365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20513308-20513593	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20494487..20497338-chr2:20512845..20515779,2	K562	blood:
2	chr2:20507108..20509449-chr2:20512530..20514676,2	K562	blood:
3	chr2:20506314..20508608-chr2:20513176..20516092,2	K562	blood:
4	chr2:20512988..20515103-chr2:20550103..20552554,2	MCF-7	breast:

Variant related genes	Relation type
PUM2	TF binding region
ENSG00000055917	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10175853	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10187080	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10192042	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10206974	0.96[ASN][1000 genomes]
rs1043400	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10460445	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10460449	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10460450	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10460451	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10856797	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11096654	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11096659	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11888357	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895228	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896241	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898408	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11900127	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902769	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11903745	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465832	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12472685	0.88[ASN][1000 genomes]
rs12473500	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12474897	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12478265	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13393733	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17612703	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072464	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2080190	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2348703	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34678899	0.87[ASN][1000 genomes]
rs3796066	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821218	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62123442	0.88[ASN][1000 genomes]
rs6748274	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785217	0.89[ASN][1000 genomes]
rs72785218	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785278	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785282	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72785295	0.81[EUR][1000 genomes]
rs72785297	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785298	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785300	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785301	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72787406	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72787409	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72787411	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787415	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787499	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787500	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72787501	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72788905	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72788906	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs741188	0.80[EUR][1000 genomes]
rs7558385	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558833	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7563245	0.82[ASN][1000 genomes]
rs7579571	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7582642	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7595266	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9306890	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9306891	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:126 , 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	chr2:20483400-20514400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:20488200-20516400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:20488400-20516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:20488400-20517000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:20489400-20517400	Weak transcription	Psoas Muscle	Psoas
23	chr2:20489800-20525800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:20491000-20513400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr2:20491400-20522600	Strong transcription	HepG2	liver
26	chr2:20491800-20513600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:20491800-20514800	Weak transcription	Gastric	stomach
28	chr2:20492400-20525800	Strong transcription	Liver	Liver
29	chr2:20496200-20513400	Strong transcription	GM12878-XiMat	blood
30	chr2:20496800-20516400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:20497400-20516600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:20499200-20527600	Weak transcription	Small Intestine	intestine
33	chr2:20500200-20522400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:20501000-20514000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:20501000-20519600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:20501600-20525000	Strong transcription	Placenta	Placenta
37	chr2:20503000-20534600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:20504200-20516400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:20505000-20513400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:20505000-20514400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:20505000-20515400	Strong transcription	Adipose Nuclei	Adipose
42	chr2:20505200-20513600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:20505200-20517400	Strong transcription	Primary B cells from cord blood	blood
44	chr2:20505200-20526000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:20505200-20526600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:20505600-20514200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:20505600-20514400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:20505600-20515000	Strong transcription	A549	lung
49	chr2:20505600-20515400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:20505600-20518200	Strong transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links