Variant report

Variant	rs62264124
Chromosome Location	chr3:112055023-112055024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112050155..112051724-chr3:112053726..112056411,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091972	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10804500	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934166	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934167	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934169	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934170	0.81[EUR][1000 genomes]
rs11708769	0.81[EUR][1000 genomes]
rs11710561	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11712036	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719721	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11917566	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11917581	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629421	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12630238	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12630278	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12633029	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12634619	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12635015	0.81[EUR][1000 genomes]
rs12635872	0.87[EUR][1000 genomes]
rs12639474	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13069751	0.86[ASN][1000 genomes]
rs1317243	0.85[ASN][1000 genomes]
rs16859469	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16859507	0.81[EUR][1000 genomes]
rs1814987	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1879511	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1879514	0.81[ASN][1000 genomes]
rs2895395	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2895396	0.81[EUR][1000 genomes]
rs4355253	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4355254	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57025230	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57661530	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58425909	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59202208	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59744939	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278831	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278832	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278833	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278834	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62278835	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278836	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278837	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278838	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278839	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278841	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278842	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278844	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278846	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62278847	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62278848	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278849	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278850	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278853	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62278854	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278855	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62278856	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6764384	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6787841	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6788309	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6789161	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6801708	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6801739	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72950242	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72950273	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72952411	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72952437	0.81[EUR][1000 genomes]
rs7639471	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639794	0.83[ASN][1000 genomes]
rs7653490	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs869042	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9834347	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863371	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9867245	0.81[EUR][1000 genomes]
rs9868582	0.90[ASN][1000 genomes]
rs9990215	0.88[ASN][1000 genomes]
rs9990216	0.88[ASN][1000 genomes]
rs9990220	0.88[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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3413622	chr3:112054745-112055084	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112051800-112055400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr3:112052600-112062400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:112052600-112066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:112052800-112076200	Weak transcription	Right Ventricle	heart
5	chr3:112053000-112056400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
6	chr3:112053000-112057200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:112053200-112062200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:112053200-112066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:112053200-112076400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:112053400-112055800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:112053400-112057200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:112053400-112057600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:112053600-112056600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:112053800-112056200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
15	chr3:112053800-112056200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:112053800-112056800	Weak transcription	HMEC	breast
17	chr3:112053800-112057000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:112053800-112057000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:112053800-112063800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:112053800-112064200	Weak transcription	Fetal Intestine Large	intestine
21	chr3:112054000-112055200	Enhancers	Fetal Intestine Small	intestine
22	chr3:112054000-112056400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:112054000-112057200	Enhancers	Adipose Nuclei	Adipose
24	chr3:112054000-112065800	Weak transcription	Fetal Kidney	kidney
25	chr3:112054000-112068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:112054200-112055200	Weak transcription	Placenta	Placenta
27	chr3:112054200-112055400	Enhancers	Fetal Lung	lung
28	chr3:112054200-112055400	Enhancers	Fetal Stomach	stomach
29	chr3:112054200-112055800	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:112054200-112056600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:112054200-112063800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:112054200-112064000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:112054400-112055400	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:112054400-112055600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
35	chr3:112054400-112056000	Enhancers	Thymus	Thymus
36	chr3:112054400-112056200	Enhancers	Aorta	Aorta
37	chr3:112054400-112056400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
38	chr3:112054400-112056600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:112054400-112058800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
40	chr3:112054400-112059200	Weak transcription	Brain Substantia Nigra	brain
41	chr3:112054600-112055400	Enhancers	H9 Cell Line	embryonic stem cell
42	chr3:112054600-112055400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:112054600-112055400	Enhancers	Brain Hippocampus Middle	brain
44	chr3:112054600-112055800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr3:112054600-112056200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:112054600-112056400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:112054600-112056600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr3:112054600-112057000	Enhancers	Brain Anterior Caudate	brain
49	chr3:112054600-112059600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:112054600-112059600	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links