Variant report

Variant	rs10848553
Chromosome Location	chr12:1802316-1802317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1772246..1773869-chr12:1801718..1803350,2	MCF-7	breast:
2	chr12:1769488..1776078-chr12:1798561..1806450,20	K562	blood:
3	chr12:918309..920299-chr12:1801890..1803898,2	K562	blood:
4	chr12:1800837..1805465-chr12:1806386..1808744,4	MCF-7	breast:
5	chr12:1801029..1803898-chr12:1875286..1877234,3	MCF-7	breast:
6	chr12:1801036..1802914-chr12:1804421..1806179,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266043	Chromatin interaction
ENSG00000271500	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1029629	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773986	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10848551	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10848552	0.99[ASN][1000 genomes]
rs10848558	0.82[AMR][1000 genomes]
rs10848569	0.85[AMR][1000 genomes]
rs11061918	0.82[ASN][1000 genomes]
rs11061919	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11061920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061921	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061923	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11061924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061925	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061927	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11061937	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11061940	0.82[AMR][1000 genomes]
rs11061957	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11061962	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11061968	0.85[AMR][1000 genomes]
rs11061974	0.84[AMR][1000 genomes]
rs1136213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11832817	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12230579	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12231894	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12342	0.81[AMR][1000 genomes]
rs12582624	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12810020	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12812707	0.85[AMR][1000 genomes]
rs12813694	0.85[AMR][1000 genomes]
rs12828908	0.85[AMR][1000 genomes]
rs12831353	0.85[AMR][1000 genomes]
rs2058034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2058035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240613	0.83[AMR][1000 genomes]
rs2286385	0.83[AMR][1000 genomes]
rs2370055	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34375871	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809266	0.83[AMR][1000 genomes]
rs4766413	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6489320	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6489323	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489324	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66590925	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7132033	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7297509	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7313760	0.85[AMR][1000 genomes]
rs7975826	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7978818	0.82[AMR][1000 genomes]
rs929434	0.85[AMR][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	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 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	chr12:1799400-1803000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr12:1799600-1802400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:1799600-1802600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:1799600-1802600	Active TSS	GM12878-XiMat	blood
5	chr12:1799800-1802400	Active TSS	Brain Anterior Caudate	brain
6	chr12:1800600-1802600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:1800600-1802800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr12:1800800-1802600	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr12:1801000-1802600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr12:1801000-1805600	Weak transcription	Pancreas	Pancrea
11	chr12:1801000-1815800	Weak transcription	Esophagus	oesophagus
12	chr12:1801000-1815800	Weak transcription	Gastric	stomach
13	chr12:1801200-1802400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:1801200-1802600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:1801200-1803200	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:1801200-1803600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:1801200-1807200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:1801400-1803600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:1801400-1804000	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:1801400-1806400	Weak transcription	Fetal Lung	lung
21	chr12:1801400-1806600	Weak transcription	Aorta	Aorta
22	chr12:1801600-1802400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:1801600-1802400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:1801600-1804000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr12:1801600-1804800	Weak transcription	Osteobl	bone
26	chr12:1801600-1805200	Weak transcription	Ovary	ovary
27	chr12:1801600-1805400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:1801600-1806000	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:1801600-1806600	Weak transcription	Fetal Brain Male	brain
30	chr12:1801600-1807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:1801600-1814200	Weak transcription	HSMM	muscle
32	chr12:1801600-1815200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:1801600-1823400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:1801600-1827800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:1801800-1802400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:1801800-1802400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:1801800-1802400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr12:1801800-1802400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:1801800-1802400	Enhancers	Fetal Intestine Large	intestine
40	chr12:1801800-1802400	Genic enhancers	Fetal Stomach	stomach
41	chr12:1801800-1802400	Enhancers	Left Ventricle	heart
42	chr12:1801800-1802400	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr12:1801800-1802400	Enhancers	HMEC	breast
44	chr12:1801800-1802400	Enhancers	HUVEC	blood vessel
45	chr12:1801800-1802600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr12:1801800-1802600	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr12:1801800-1802600	Enhancers	Psoas Muscle	Psoas
48	chr12:1801800-1802800	Enhancers	Primary hematopoietic stem cells	blood
49	chr12:1801800-1803000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:1801800-1804200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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