Variant report

Variant	rs2649896
Chromosome Location	chr12:123238797-123238798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr12:123238495-123238852	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:123238781-123238799	MCF-7	breast:	n/a	n/a
3	POLR2A	chr12:123238528-123238874	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:123236975-123238829	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:123238765-123238940	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123120793..123122502-chr12:123237496..123239283,2	MCF-7	breast:
2	chr12:123236945..123239092-chr12:123263522..123266278,3	K562	blood:
3	chr12:123106486..123108264-chr12:123238733..123241698,2	K562	blood:
4	chr12:123236169..123239442-chr12:123257222..123260625,5	MCF-7	breast:
5	chr12:122883132..122886264-chr12:123235650..123239708,3	MCF-7	breast:
6	chr12:123237435..123239674-chr12:123244773..123246396,2	K562	blood:
7	chr12:122984002..122986497-chr12:123237253..123240252,3	MCF-7	breast:
8	chr12:123237859..123240331-chr12:123248659..123250733,2	K562	blood:
9	chr12:123237222..123239251-chr12:123250581..123253691,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000256044	TF binding region
ENSG00000130779	Chromatin interaction
ENSG00000130783	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000206914	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1026395	1.00[JPT][hapmap]
rs1037593	1.00[JPT][hapmap]
rs10773599	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs10847742	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs10847749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs10847751	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10847775	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs10847910	1.00[JPT][hapmap]
rs11059729	1.00[ASN][1000 genomes]
rs11060152	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11060932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1260121	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671684	1.00[JPT][hapmap]
rs1671687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1696355	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061099	1.00[JPT][hapmap]
rs2343107	1.00[JPT][hapmap]
rs2649894	0.87[ASN][1000 genomes]
rs2649895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649900	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649914	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs4307760	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4759353	1.00[JPT][hapmap]
rs4759354	1.00[JPT][hapmap]
rs4759384	1.00[JPT][hapmap]
rs4759438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs548349	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489241	1.00[CEU][hapmap]
rs651683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138257	1.00[JPT][hapmap]
rs7298176	1.00[JPT][hapmap]
rs7306948	1.00[JPT][hapmap]
rs7485652	1.00[JPT][hapmap]
rs7957643	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7958155	1.00[JPT][hapmap]
rs839354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839355	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839356	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839357	1.00[ASN][1000 genomes]
rs839362	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs897386	0.81[CEU][hapmap]
rs897388	1.00[JPT][hapmap]
rs967281	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs9795629	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2649896	TMEM120B	cis	parietal	SCAN
rs2649896	RAB35	cis	parietal	SCAN
rs2649896	KDM2B	cis	cerebellum	SCAN
rs2649896	EIF2B1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123237800-123238800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:123237800-123238800	Flanking Active TSS	Brain Germinal Matrix	brain
3	chr12:123237800-123238800	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr12:123237800-123238800	Flanking Active TSS	Fetal Brain Female	brain
5	chr12:123237800-123238800	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr12:123238000-123238800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
7	chr12:123238000-123238800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:123238000-123238800	Flanking Active TSS	Fetal Brain Male	brain
9	chr12:123238000-123238800	Flanking Active TSS	Hela-S3	cervix
10	chr12:123238000-123239000	Transcr. at gene 5' and 3'	A549	lung
11	chr12:123238200-123238800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:123238200-123238800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:123238200-123238800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:123238200-123238800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:123238200-123238800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
16	chr12:123238200-123238800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
17	chr12:123238200-123238800	Genic enhancers	Primary B cells from peripheral blood	blood
18	chr12:123238200-123238800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:123238200-123238800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:123238200-123238800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:123238200-123238800	Enhancers	Esophagus	oesophagus
22	chr12:123238200-123238800	Genic enhancers	Placenta	Placenta
23	chr12:123238200-123238800	Enhancers	Gastric	stomach
24	chr12:123238200-123238800	Enhancers	Left Ventricle	heart
25	chr12:123238200-123238800	Enhancers	Pancreas	Pancrea
26	chr12:123238200-123238800	Enhancers	Small Intestine	intestine
27	chr12:123238200-123238800	Genic enhancers	Spleen	Spleen
28	chr12:123238200-123238800	Transcr. at gene 5' and 3'	NHLF	lung
29	chr12:123238200-123239000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
30	chr12:123238200-123239000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:123238200-123242600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:123238200-123249400	Weak transcription	Aorta	Aorta
33	chr12:123238400-123238800	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
34	chr12:123238400-123238800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:123238400-123238800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
36	chr12:123238400-123238800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:123238400-123238800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr12:123238400-123238800	Genic enhancers	Primary B cells from cord blood	blood
39	chr12:123238400-123238800	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr12:123238400-123238800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:123238400-123238800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:123238400-123238800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
43	chr12:123238400-123238800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:123238400-123238800	Genic enhancers	Liver	Liver
45	chr12:123238400-123238800	Genic enhancers	Brain Cingulate Gyrus	brain
46	chr12:123238400-123238800	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
47	chr12:123238400-123238800	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
48	chr12:123238400-123238800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:123238400-123238800	Genic enhancers	Brain Substantia Nigra	brain
50	chr12:123238400-123238800	Active TSS	Colonic Mucosa	Colon

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