Variant report

Variant	rs73241999
Chromosome Location	chr12:9236247-9236248
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr12:9236158-9236928	U2OS	brain:	n/a	n/a
2	POLR2A	chr12:9236048-9237557	HepG2	liver:	n/a	n/a
3	KAP1	chr12:9236226-9236894	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9236127..9237912-chr12:9246166..9247720,2	MCF-7	breast:
2	chr12:9217388..9219245-chr12:9235426..9237537,2	MCF-7	breast:

Variant related genes	Relation type
A2M	TF binding region
ENSG00000245105	Chromatin interaction
ENSG00000214851	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11831631	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11831793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11832509	1.00[AMR][1000 genomes]
rs11833184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11833893	1.00[AMR][1000 genomes]
rs1805684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1805686	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1805694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3026223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3026224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3026228	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3026231	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35040316	1.00[AMR][1000 genomes]
rs57018529	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58097118	1.00[AMR][1000 genomes]
rs58565807	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60105910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60289110	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73240200	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73240201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73241907	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73241991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73246318	1.00[AMR][1000 genomes]
rs73246327	1.00[AMR][1000 genomes]
rs73246334	1.00[AMR][1000 genomes]
rs73246337	1.00[AMR][1000 genomes]
rs73246344	1.00[AMR][1000 genomes]
rs73246352	1.00[AMR][1000 genomes]
rs73246383	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
2	chr12:9218400-9236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:9218400-9236600	Weak transcription	Brain Substantia Nigra	brain
4	chr12:9218400-9237200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:9218600-9236400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
7	chr12:9230800-9240400	Weak transcription	Placenta	Placenta
8	chr12:9230800-9243600	Weak transcription	Colonic Mucosa	Colon
9	chr12:9232200-9264600	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:9232400-9242600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:9232400-9244600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:9232600-9236400	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:9233200-9236400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:9234000-9237400	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:9234400-9236800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr12:9234400-9237800	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:9234600-9239400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr12:9235000-9242800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:9235000-9253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:9235200-9236400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:9235200-9236400	Weak transcription	Right Ventricle	heart
22	chr12:9235200-9236600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:9235200-9241200	Weak transcription	Left Ventricle	heart
24	chr12:9235200-9242400	Weak transcription	Aorta	Aorta
25	chr12:9235200-9242400	Weak transcription	Ovary	ovary
26	chr12:9235200-9242800	Weak transcription	Fetal Stomach	stomach
27	chr12:9235200-9242800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:9235200-9242800	Weak transcription	Spleen	Spleen
29	chr12:9235200-9243000	Weak transcription	Lung	lung
30	chr12:9235200-9265800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:9235400-9236400	Weak transcription	Adipose Nuclei	Adipose
32	chr12:9235800-9241600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:9236000-9237600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:9236200-9236600	ZNF genes & repeats	Fetal Heart	heart
35	chr12:9236200-9236600	Genic enhancers	HepG2	liver
36	chr12:9236200-9236800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
37	chr12:9236200-9236800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
38	chr12:9236200-9237000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
39	chr12:9236200-9237200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:9236200-9237200	ZNF genes & repeats	Liver	Liver
41	chr12:9236200-9237200	ZNF genes & repeats	Psoas Muscle	Psoas
42	chr12:9236200-9237400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
43	chr12:9236200-9237600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:9236200-9237600	ZNF genes & repeats	Fetal Lung	lung

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