Variant report

Variant	rs12472775
Chromosome Location	chr2:10548037-10548038
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10546361..10548210-chr2:10629662..10631779,2	MCF-7	breast:
2	chr2:10261171..10265935-chr2:10544190..10551018,10	K562	blood:
3	chr2:10440924..10446095-chr2:10544022..10551736,19	MCF-7	breast:
4	chr2:10418216..10420909-chr2:10547555..10550904,3	K562	blood:
5	chr2:10472884..10475562-chr2:10547169..10549759,2	K562	blood:
6	chr2:10272011..10278010-chr2:10546327..10552012,10	K562	blood:
7	chr2:10445047..10447239-chr2:10547484..10549906,2	MCF-7	breast:
8	chr2:10535464..10537756-chr2:10546210..10548957,2	K562	blood:
9	chr2:10416484..10418101-chr2:10547563..10549707,2	MCF-7	breast:
10	chr2:10266037..10268714-chr2:10547903..10550604,2	K562	blood:
11	chr2:10442822..10444429-chr2:10547773..10549369,2	K562	blood:
12	chr2:10543371..10546081-chr2:10546266..10548397,3	K562	blood:
13	chr2:10423718..10426925-chr2:10546888..10550753,3	MCF-7	breast:
14	chr2:10528409..10530378-chr2:10546581..10548332,2	MCF-7	breast:
15	chr2:10409606..10412546-chr2:10546766..10549181,2	MCF-7	breast:
16	chr2:10531124..10533976-chr2:10546440..10548143,2	MCF-7	breast:
17	chr2:10537541..10541103-chr2:10547321..10550436,3	MCF-7	breast:
18	chr2:10436642..10438745-chr2:10547775..10550649,2	K562	blood:
19	chr2:10546313..10548622-chr2:10549795..10552775,2	K562	blood:
20	chr2:10543950..10547023-chr2:10547884..10550475,4	MCF-7	breast:
21	chr2:10397007..10398752-chr2:10545824..10548279,2	MCF-7	breast:
22	chr2:10535204..10537517-chr2:10547562..10550495,2	MCF-7	breast:
23	chr2:10498534..10501300-chr2:10547746..10549393,2	K562	blood:
24	chr2:10538831..10544260-chr2:10544573..10548851,6	K562	blood:
25	chr2:10547842..10550365-chr2:10556156..10557846,2	K562	blood:
26	chr2:10394375..10395994-chr2:10546875..10548738,2	K562	blood:
27	chr2:10266037..10269086-chr2:10547903..10550826,4	K562	blood:
28	chr2:10460038..10463230-chr2:10546392..10550535,3	MCF-7	breast:
29	chr2:10270635..10275854-chr2:10544682..10552679,11	K562	blood:
30	chr2:10546025..10548259-chr2:10592640..10594576,2	MCF-7	breast:
31	chr2:10440762..10444214-chr2:10546694..10551810,5	K562	blood:
32	chr2:10259324..10265273-chr2:10547206..10552383,9	K562	blood:
33	chr2:10546710..10550413-chr2:10585616..10590159,6	K562	blood:
34	chr2:10547359..10549276-chr2:10571069..10572635,2	MCF-7	breast:
35	chr2:10392994..10395994-chr2:10546875..10548738,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257135	Chromatin interaction
ENSG00000115756	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000264030	Chromatin interaction
ENSG00000272524	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10189719	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467741	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808315	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35158739	0.85[ASN][1000 genomes]
rs3755263	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755264	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771128	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771129	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3771134	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771138	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62130186	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62130189	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62130190	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs876614	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876615	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs876616	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873643	chr2:10535481-10583160	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv873644	chr2:10537347-10576424	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10533000-10551800	Weak transcription	Ovary	ovary
2	chr2:10533400-10549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:10541200-10550800	Enhancers	Fetal Muscle Leg	muscle
4	chr2:10542000-10549400	Enhancers	HUVEC	blood vessel
5	chr2:10542400-10549400	Enhancers	NHDF-Ad	bronchial
6	chr2:10544200-10549600	Enhancers	Left Ventricle	heart
7	chr2:10544200-10549800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:10544400-10548800	Enhancers	Esophagus	oesophagus
9	chr2:10544400-10549800	Enhancers	Right Ventricle	heart
10	chr2:10544600-10548200	Bivalent Enhancer	Placenta	Placenta
11	chr2:10544600-10548600	Enhancers	Liver	Liver
12	chr2:10544600-10549400	Enhancers	Right Atrium	heart
13	chr2:10544800-10548800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:10544800-10549600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:10544800-10549600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:10544800-10549800	Enhancers	Lung	lung
17	chr2:10545000-10548400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:10545200-10548400	Enhancers	Stomach Mucosa	stomach
19	chr2:10545200-10549800	Enhancers	Pancreas	Pancrea
20	chr2:10545400-10549200	Enhancers	Thymus	Thymus
21	chr2:10545400-10549600	Enhancers	Spleen	Spleen
22	chr2:10545400-10551800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:10545600-10548200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:10545600-10548200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:10545600-10549600	Enhancers	NH-A	brain
26	chr2:10545600-10549800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:10545800-10548200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr2:10545800-10548400	Weak transcription	NHLF	lung
29	chr2:10545800-10548600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:10545800-10549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:10545800-10549800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr2:10545800-10550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:10546000-10548600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr2:10546000-10549400	Enhancers	Osteobl	bone
35	chr2:10546200-10548200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr2:10546200-10548200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr2:10546200-10548200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr2:10546200-10548400	Weak transcription	Fetal Kidney	kidney
39	chr2:10546200-10549000	Enhancers	Psoas Muscle	Psoas
40	chr2:10546200-10549800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr2:10546200-10550600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:10546400-10548200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:10546400-10548200	Enhancers	Primary B cells from cord blood	blood
44	chr2:10546400-10548200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:10546400-10548200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:10546400-10548200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:10546400-10549000	Weak transcription	Brain Germinal Matrix	brain
48	chr2:10546400-10551400	Enhancers	Fetal Thymus	thymus
49	chr2:10546600-10548400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:10546600-10549200	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links