Variant report

Variant	rs672697
Chromosome Location	chr12:50413015-50413016
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50412978-50413031	MCF-7	breast:	n/a	n/a
2	ZNF143	chr12:50412751-50413082	K562	blood:	n/a	n/a
3	MAZ	chr12:50412893-50413098	K562	blood:	n/a	n/a
4	RCOR1	chr12:50412820-50413114	K562	blood:	n/a	n/a
5	EP300	chr12:50412823-50413123	K562	blood:	n/a	n/a
6	BHLHE40	chr12:50412903-50413058	K562	blood:	n/a	n/a
7	GATA3	chr12:50412960-50413300	SH-SY5Y	brain:	n/a	chr12:50413010-50413020
8	ATF1	chr12:50412854-50413081	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50409191..50412092-chr12:50412354..50415044,3	K562	blood:
2	chr12:50402113..50404435-chr12:50411266..50413680,2	K562	blood:
3	chr12:50410919..50413277-chr12:50413470..50417179,5	K562	blood:
4	chr12:50395341..50399448-chr12:50410625..50413867,3	K562	blood:
5	chr12:50406498..50409070-chr12:50412781..50414951,2	K562	blood:
6	chr12:50394516..50396825-chr12:50410835..50413613,2	MCF-7	breast:
7	chr12:50410558..50416843-chr12:50417238..50421054,9	MCF-7	breast:
8	chr12:50412413..50416457-chr12:50416971..50420566,5	MCF-7	breast:

No data

Variant related genes	Relation type
RACGAP1	TF binding region
ENSG00000161800	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11169179	1.00[EUR][1000 genomes]
rs11169181	1.00[EUR][1000 genomes]
rs11169272	1.00[AMR][1000 genomes]
rs11169273	1.00[AMR][1000 genomes]
rs11169279	1.00[AMR][1000 genomes]
rs11169280	1.00[AMR][1000 genomes]
rs12299109	1.00[AMR][1000 genomes]
rs12305438	1.00[AMR][1000 genomes]
rs12309501	1.00[AMR][1000 genomes]
rs12316969	1.00[EUR][1000 genomes]
rs12318294	1.00[EUR][1000 genomes]
rs2697111	1.00[EUR][1000 genomes]
rs296735	1.00[AMR][1000 genomes]
rs296738	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs296748	1.00[EUR][1000 genomes]
rs296749	1.00[EUR][1000 genomes]
rs296753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs296755	1.00[EUR][1000 genomes]
rs296757	1.00[EUR][1000 genomes]
rs296758	1.00[EUR][1000 genomes]
rs296761	1.00[EUR][1000 genomes]
rs296764	1.00[EUR][1000 genomes]
rs296765	1.00[EUR][1000 genomes]
rs372753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs425726	1.00[EUR][1000 genomes]
rs455037	1.00[EUR][1000 genomes]
rs55800109	1.00[AMR][1000 genomes]
rs57143574	1.00[AMR][1000 genomes]
rs57596053	1.00[AMR][1000 genomes]
rs58826760	1.00[AMR][1000 genomes]
rs60009415	1.00[EUR][1000 genomes]
rs61221429	1.00[AMR][1000 genomes]
rs7312996	1.00[AMR][1000 genomes]
rs73310966	1.00[EUR][1000 genomes]
rs74090092	1.00[AMR][1000 genomes]
rs74090094	1.00[AMR][1000 genomes]
rs74092539	1.00[AMR][1000 genomes]
rs7963427	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
5	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases
7	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
8	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50369600-50418200	Weak transcription	Colonic Mucosa	Colon
2	chr12:50382000-50414800	Weak transcription	Psoas Muscle	Psoas
3	chr12:50383000-50418000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:50388200-50418000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:50391000-50418000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:50392800-50418200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:50399200-50418200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr12:50399800-50417400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:50400400-50418200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:50400600-50418200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:50401200-50418200	Weak transcription	Primary B cells from cord blood	blood
12	chr12:50403000-50418600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:50407800-50415000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:50407800-50418000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:50408400-50415000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:50408400-50418000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:50408600-50416400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:50408600-50417000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:50408600-50417600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:50409000-50418000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:50409200-50417600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:50409200-50418000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:50409200-50418200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:50409200-50418400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:50409400-50414400	Weak transcription	GM12878-XiMat	blood
26	chr12:50409400-50418000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:50409800-50418400	Weak transcription	Primary T cells from cord blood	blood
28	chr12:50410000-50418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:50410200-50415000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:50410200-50415200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:50410200-50418200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:50410600-50418000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:50410600-50418000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:50410600-50418600	Weak transcription	Spleen	Spleen
35	chr12:50411200-50413200	Enhancers	NHLF	lung
36	chr12:50411200-50413400	Enhancers	HepG2	liver
37	chr12:50411200-50414400	Weak transcription	HSMMtube	muscle
38	chr12:50411200-50415000	Weak transcription	NHEK	skin
39	chr12:50411200-50415200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:50411200-50415600	Weak transcription	Brain Germinal Matrix	brain
41	chr12:50411200-50416400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:50411200-50418200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:50411200-50418200	Weak transcription	Thymus	Thymus
44	chr12:50411200-50418600	Weak transcription	Small Intestine	intestine
45	chr12:50411400-50413400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:50411400-50413400	Enhancers	NHDF-Ad	bronchial
47	chr12:50411400-50413400	Enhancers	Osteobl	bone
48	chr12:50411400-50414400	Weak transcription	Fetal Kidney	kidney
49	chr12:50411400-50414800	Weak transcription	Brain Substantia Nigra	brain
50	chr12:50411400-50414800	Weak transcription	HSMM	muscle

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