Variant report

Variant	rs56967344
Chromosome Location	chr12:48098876-48098877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr12:48098475-48101043	K562	blood:	n/a	chr12:48099629-48099638
2	TCF12	chr12:48098698-48100317	A549	lung:	n/a	n/a
3	MXI1	chr12:48098821-48101083	SK-N-SH	brain:	n/a	chr12:48099085-48099100
4	MAZ	chr12:48098580-48100465	IMR90	lung:	n/a	chr12:48099846-48099856

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48090015..48092688-chr12:48097959..48099858,2	MCF-7	breast:
2	chr12:48098316..48105030-chr12:48164986..48170762,10	K562	blood:
3	chr12:48098678..48101690-chr12:48212441..48216325,5	MCF-7	breast:
4	chr12:48094047..48097465-chr12:48098016..48100930,6	MCF-7	breast:
5	chr12:48098389..48101858-chr12:48164679..48169908,6	MCF-7	breast:
6	chr12:48097907..48100262-chr12:48151350..48154397,3	K562	blood:
7	chr12:48058375..48060319-chr12:48098023..48100043,2	K562	blood:
8	chr12:48097267..48105309-chr12:48111877..48120917,8	MCF-7	breast:
9	chr12:48098499..48101428-chr12:48108711..48111511,2	MCF-7	breast:
10	chr12:48098184..48101263-chr12:48165431..48167554,3	MCF-7	breast:

No data

Variant related genes	Relation type
RPAP3	TF binding region
ENSG00000257433	TF binding region
ENSG00000061273	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000111405	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000211584	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10492007	1.00[AMR][1000 genomes]
rs17122136	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17122138	0.87[AMR][1000 genomes]
rs2100808	1.00[AMR][1000 genomes]
rs36123489	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4348981	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4550297	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56915320	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57671593	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58292976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58702884	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59702452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60739072	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60873325	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61702904	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs716665	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7298221	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7311790	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7315257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73298686	1.00[AMR][1000 genomes]
rs73298687	1.00[AMR][1000 genomes]
rs73298689	0.87[AMR][1000 genomes]
rs73300611	0.89[AMR][1000 genomes]
rs73300632	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300647	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300650	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300653	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300658	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73300663	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300666	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300680	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs748306	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7962695	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7964752	0.91[AFR][1000 genomes];1.00[AMR][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	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
2	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48046600-48099200	Weak transcription	Gastric	stomach
2	chr12:48046800-48099000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48056000-48099000	Weak transcription	Right Ventricle	heart
4	chr12:48063000-48099000	Weak transcription	Small Intestine	intestine
5	chr12:48064600-48099200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:48074200-48099000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:48083800-48099200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:48086800-48099000	Weak transcription	Lung	lung
9	chr12:48087000-48099000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48094800-48099000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:48094800-48099000	Weak transcription	Aorta	Aorta
12	chr12:48094800-48099000	Weak transcription	Ovary	ovary
13	chr12:48097000-48099000	Enhancers	Primary B cells from peripheral blood	blood
14	chr12:48097200-48099000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:48097600-48099000	Weak transcription	Left Ventricle	heart
16	chr12:48097600-48099000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:48097600-48099200	Enhancers	Spleen	Spleen
18	chr12:48097600-48101000	Active TSS	GM12878-XiMat	blood
19	chr12:48098000-48099000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:48098000-48099000	Enhancers	Liver	Liver
21	chr12:48098400-48099000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:48098400-48099200	Flanking Active TSS	Dnd41	blood
23	chr12:48098600-48099000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:48098600-48099000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:48098600-48099000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr12:48098600-48099000	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:48098600-48099000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:48098600-48099000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:48098600-48099000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:48098600-48099000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:48098600-48099000	Enhancers	Fetal Muscle Trunk	muscle
32	chr12:48098600-48099000	Enhancers	Placenta	Placenta
33	chr12:48098600-48099000	Enhancers	Pancreas	Pancrea
34	chr12:48098600-48099000	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr12:48098600-48099200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:48098600-48099200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr12:48098600-48099200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:48098600-48099200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr12:48098600-48099200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:48098600-48099200	Flanking Active TSS	Hela-S3	cervix
41	chr12:48098600-48099200	Flanking Active TSS	K562	blood
42	chr12:48098600-48099400	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr12:48098600-48099400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr12:48098600-48099400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr12:48098600-48099400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr12:48098600-48099400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:48098600-48100200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr12:48098600-48100200	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr12:48098600-48100400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:48098600-48100400	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links