Variant report

Variant	rs10848539
Chromosome Location	chr12:1743556-1743557
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1738742..1741489-chr12:1743344..1746284,2	K562	blood:
2	chr12:1741511..1744510-chr12:1943871..1945697,2	K562	blood:
3	chr12:1741431..1743986-chr12:1900425..1902270,2	MCF-7	breast:
4	chr12:1738204..1740242-chr12:1742756..1744844,2	K562	blood:
5	chr12:1743461..1744388-chr12:1899911..1900896,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111186	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10773972	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061888	0.85[EUR][1000 genomes]
rs2079516	0.84[EUR][1000 genomes]
rs2270032	0.89[EUR][1000 genomes]
rs2270033	0.91[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4765836	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4766401	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs6489308	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv826180	chr12:1614395-1759431	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv826181	chr12:1619798-1754941	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	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
7	nsv898587	chr12:1732295-1756642	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv898588	chr12:1736314-1755960	Bivalent Enhancer Enhancers Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv556994	chr12:1737309-1743843	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv898589	chr12:1738111-1755654	Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv898590	chr12:1740171-1757743	Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1733000-1744000	Weak transcription	K562	blood
2	chr12:1739800-1753800	Weak transcription	Esophagus	oesophagus
3	chr12:1740000-1744000	Weak transcription	Aorta	Aorta
4	chr12:1740000-1748800	Weak transcription	Pancreas	Pancrea
5	chr12:1740000-1749000	Weak transcription	Ovary	ovary
6	chr12:1740200-1745000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:1740400-1743800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:1740400-1744000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:1740400-1744200	Enhancers	Adipose Nuclei	Adipose
10	chr12:1740600-1743600	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:1740600-1745600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:1740600-1748800	Weak transcription	Gastric	stomach
13	chr12:1740600-1753400	Strong transcription	Osteobl	bone
14	chr12:1740600-1755000	Weak transcription	Spleen	Spleen
15	chr12:1740800-1744400	Enhancers	Fetal Brain Male	brain
16	chr12:1740800-1747200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:1740800-1751000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:1740800-1753200	Weak transcription	NH-A	brain
19	chr12:1740800-1753600	Weak transcription	Placenta	Placenta
20	chr12:1740800-1757400	Weak transcription	GM12878-XiMat	blood
21	chr12:1741000-1743600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:1741000-1743600	Strong transcription	Fetal Stomach	stomach
23	chr12:1741000-1744000	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr12:1741000-1744000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:1741000-1749200	Weak transcription	HSMMtube	muscle
26	chr12:1741400-1745600	Enhancers	Liver	Liver
27	chr12:1741400-1752800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:1741600-1743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:1741600-1745200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr12:1741800-1744000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:1741800-1745000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:1741800-1746000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr12:1742000-1744000	Strong transcription	NHLF	lung
34	chr12:1742000-1753400	Weak transcription	NHEK	skin
35	chr12:1742200-1743600	Weak transcription	Brain Anterior Caudate	brain
36	chr12:1742200-1743600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr12:1742200-1743600	Weak transcription	Brain Substantia Nigra	brain
38	chr12:1742200-1743800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:1742200-1743800	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:1742200-1744000	Weak transcription	Brain Angular Gyrus	brain
41	chr12:1742200-1744200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:1742200-1744600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr12:1742200-1745000	Enhancers	Fetal Brain Female	brain
44	chr12:1742200-1745200	Enhancers	Brain Germinal Matrix	brain
45	chr12:1742200-1749400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:1742400-1743800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr12:1742400-1743800	Weak transcription	Left Ventricle	heart
48	chr12:1742400-1744400	Genic enhancers	Fetal Muscle Leg	muscle
49	chr12:1742400-1747400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:1742600-1743800	Weak transcription	Right Atrium	heart

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