Variant report

Variant	rs855275
Chromosome Location	chr12:48001770-48001771
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC48A1-4	chr12:48001617-48001971	NONHSAT027928

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1034733	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615607	0.92[EUR][1000 genomes]
rs11615629	0.92[EUR][1000 genomes]
rs1232978	0.87[ASN][1000 genomes]
rs1233048	0.85[EUR][1000 genomes]
rs1233054	0.83[EUR][1000 genomes]
rs1233056	0.83[EUR][1000 genomes]
rs1233057	0.83[EUR][1000 genomes]
rs1233060	0.83[EUR][1000 genomes]
rs1233062	0.84[GIH][hapmap];1.00[JPT][hapmap]
rs1238777	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010734	0.81[EUR][1000 genomes]
rs2025	0.85[EUR][1000 genomes]
rs74085940	0.86[ASN][1000 genomes]
rs757282	0.84[GIH][hapmap]
rs855271	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855278	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855279	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886431	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv832400	chr12:47840248-48024605	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1051131	chr12:47883981-48016556	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv899056	chr12:47940764-48012390	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv558786	chr12:47942029-48044011	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv558788	chr12:47945797-48012390	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2761737	chr12:47946795-48045722	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1053061	chr12:47946795-48045722	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv899057	chr12:47947551-48012390	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv527728	chr12:47954597-48044506	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47992600-48006600	Weak transcription	HSMMtube	muscle
2	chr12:47996000-48006800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:47997000-48005000	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:47998800-48030800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:47999200-48002600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:47999600-48006400	Weak transcription	Primary T cells from cord blood	blood
7	chr12:48000800-48002600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:48001000-48002000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:48001000-48002600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:48001000-48004400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr12:48001200-48002200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
12	chr12:48001400-48001800	ZNF genes & repeats	Psoas Muscle	Psoas
13	chr12:48001400-48002000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:48001400-48002600	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr12:48001600-48001800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:48001600-48002400	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:48001600-48002600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:48001600-48002600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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