Variant report

Variant	rs72787411
Chromosome Location	chr2:20486326-20486327
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20484550..20486934-chr2:20490044..20492996,3	MCF-7	breast:
2	chr2:20482981..20486539-chr2:20487663..20489842,4	MCF-7	breast:
3	chr2:20478789..20484582-chr2:20484927..20489294,7	K562	blood:
4	chr2:20474838..20476628-chr2:20486157..20488618,2	K562	blood:
5	chr2:20421775..20427916-chr2:20486064..20491550,11	MCF-7	breast:
6	chr2:20484989..20487523-chr2:20496339..20498014,2	K562	blood:

Variant related genes	Relation type
ENSG00000115884	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];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10187080	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10192042	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10206974	0.95[ASN][1000 genomes]
rs1043400	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10460445	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10460449	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10460450	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10460451	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10856797	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11096654	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11096659	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11888357	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11895228	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11896241	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11898408	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11900127	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902769	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11903745	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12465832	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12472685	0.89[ASN][1000 genomes]
rs12473500	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12474897	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12478265	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13393733	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17612703	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072464	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2080190	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2110410	0.81[EUR][1000 genomes]
rs2348703	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2820	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34678899	0.88[ASN][1000 genomes]
rs3796066	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821218	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62123442	0.89[ASN][1000 genomes]
rs6748274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72785217	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72785218	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72785278	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72785282	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72785295	0.85[EUR][1000 genomes]
rs72785297	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72785298	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72785300	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72785301	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72787406	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787409	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787415	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787433	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787499	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787500	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72787501	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72788905	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72788906	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs741188	0.84[EUR][1000 genomes]
rs7558385	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558833	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7563245	0.83[ASN][1000 genomes]
rs7579571	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7582642	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7595266	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9306890	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9306891	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20442000-20491000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20444400-20489000	Weak transcription	Stomach Mucosa	stomach
3	chr2:20454200-20488800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:20454200-20490800	Weak transcription	Right Ventricle	heart
5	chr2:20454200-20491000	Weak transcription	Gastric	stomach
6	chr2:20454200-20491000	Weak transcription	Spleen	Spleen
7	chr2:20454200-20499600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:20456400-20488800	Weak transcription	Small Intestine	intestine
9	chr2:20458000-20491000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:20460200-20528600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:20465600-20500400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:20466000-20530400	Strong transcription	Fetal Thymus	thymus
13	chr2:20467000-20522400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:20467200-20526200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr2:20467600-20490600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:20467800-20491400	Weak transcription	Lung	lung
17	chr2:20469600-20486400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:20471800-20522600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:20471800-20533800	Strong transcription	Dnd41	blood
20	chr2:20472000-20491800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:20474600-20528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:20474800-20487000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:20475400-20522400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:20476200-20514400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:20476400-20488000	Strong transcription	A549	lung
26	chr2:20476400-20488000	Strong transcription	Hela-S3	cervix
27	chr2:20476400-20491000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:20476400-20492800	Strong transcription	GM12878-XiMat	blood
29	chr2:20476400-20500000	Strong transcription	Placenta	Placenta
30	chr2:20476400-20521000	Strong transcription	Fetal Intestine Large	intestine
31	chr2:20476600-20486400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:20476600-20487400	Strong transcription	Liver	Liver
33	chr2:20476600-20490600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:20476600-20490600	Strong transcription	Primary hematopoietic stem cells	blood
35	chr2:20476600-20492000	Strong transcription	Primary B cells from cord blood	blood
36	chr2:20476600-20500600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:20476600-20516400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:20476600-20524800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:20476600-20526600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr2:20476800-20487800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:20476800-20488400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:20476800-20490400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr2:20476800-20491000	Strong transcription	HepG2	liver
44	chr2:20476800-20516800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:20477800-20486600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:20478200-20486400	Strong transcription	Primary T cells from cord blood	blood
47	chr2:20478600-20516600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:20479800-20488200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:20480000-20491000	Weak transcription	Fetal Heart	heart
50	chr2:20480400-20515400	Strong transcription	Rectal Mucosa Donor 31	rectum

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