Variant report

Variant	rs73096578
Chromosome Location	chr12:40017872-40017873
allele	C/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	NFIC	chr12:40017695-40018191	GM12878	blood:	n/a	n/a
2	ATF2	chr12:40017634-40018151	GM12878	blood:	n/a	n/a
3	ATF1	chr12:40017728-40018001	K562	blood:	n/a	n/a
4	MEF2A	chr12:40017701-40018033	GM12878	blood:	n/a	chr12:40017857-40017868 chr12:40017854-40017869 chr12:40017850-40017871
5	RUNX3	chr12:40017610-40018105	GM12878	blood:	n/a	n/a
6	MEF2C	chr12:40017685-40018124	GM12878	blood:	n/a	chr12:40017857-40017868 chr12:40017850-40017871
7	EBF1	chr12:40017769-40017991	GM12878	blood:	n/a	n/a
8	CREB1	chr12:40017673-40018269	GM12878	blood:	n/a	n/a
9	ATF2	chr12:40017642-40018058	GM12878	blood:	n/a	n/a
10	FOS	chr12:40017737-40017937	MCF10A-Er-Src	breast:	n/a	n/a
11	MEF2A	chr12:40017677-40018041	K562	blood:	n/a	chr12:40017857-40017868 chr12:40017854-40017869 chr12:40017850-40017871
12	NFATC1	chr12:40017684-40018091	GM12878	blood:	n/a	chr12:40018010-40018024
13	FOXM1	chr12:40017636-40018114	GM12878	blood:	n/a	n/a
14	MEF2A	chr12:40017683-40018080	GM12878	blood:	n/a	chr12:40017857-40017868 chr12:40017854-40017869 chr12:40017850-40017871

Variant related genes	Relation type
C12orf40	TF binding region
ABCD2	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1567738	1.00[AMR][1000 genomes]
rs58831669	0.85[AFR][1000 genomes]
rs60093332	0.85[AFR][1000 genomes]
rs7305817	0.81[AFR][1000 genomes]
rs73086888	1.00[AMR][1000 genomes]
rs73086895	1.00[AMR][1000 genomes]
rs73086896	1.00[AMR][1000 genomes]
rs73087812	0.85[AFR][1000 genomes]
rs73087865	0.85[AFR][1000 genomes]
rs73088803	1.00[AMR][1000 genomes]
rs73088804	1.00[AMR][1000 genomes]
rs73088806	1.00[AMR][1000 genomes]
rs73088808	1.00[AMR][1000 genomes]
rs73088811	1.00[AMR][1000 genomes]
rs73088812	1.00[AMR][1000 genomes]
rs73092112	0.80[AFR][1000 genomes]
rs73094416	1.00[AMR][1000 genomes]
rs73094426	1.00[AMR][1000 genomes]
rs73094430	1.00[AMR][1000 genomes]
rs73094441	1.00[AMR][1000 genomes]
rs73094443	1.00[AMR][1000 genomes]
rs73094451	1.00[AMR][1000 genomes]
rs73094465	1.00[AMR][1000 genomes]
rs73094466	1.00[AMR][1000 genomes]
rs73094469	1.00[AMR][1000 genomes]
rs73094480	1.00[AMR][1000 genomes]
rs73094482	1.00[AMR][1000 genomes]
rs73094497	1.00[AMR][1000 genomes]
rs73094498	1.00[AMR][1000 genomes]
rs73094499	1.00[AMR][1000 genomes]
rs73094502	1.00[AMR][1000 genomes]
rs73095613	0.85[AFR][1000 genomes]
rs73095657	0.85[AFR][1000 genomes]
rs73096503	1.00[AMR][1000 genomes]
rs73096504	1.00[AMR][1000 genomes]
rs73096507	1.00[AMR][1000 genomes]
rs73096509	1.00[AMR][1000 genomes]
rs73096513	1.00[AMR][1000 genomes]
rs73096521	1.00[AMR][1000 genomes]
rs73096524	1.00[AMR][1000 genomes]
rs73096528	1.00[AMR][1000 genomes]
rs73096539	1.00[AMR][1000 genomes]
rs73096542	1.00[AMR][1000 genomes]
rs73096551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73096571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73098557	0.85[AFR][1000 genomes]
rs73098572	0.85[AFR][1000 genomes]
rs73098577	0.85[AFR][1000 genomes]
rs73098599	0.85[AFR][1000 genomes]
rs73102528	0.85[AFR][1000 genomes]
rs73102537	0.85[AFR][1000 genomes]
rs73102556	0.81[AFR][1000 genomes]
rs73102559	0.81[AFR][1000 genomes]
rs73102562	0.81[AFR][1000 genomes]
rs73102575	0.80[AFR][1000 genomes]
rs7311368	0.85[AFR][1000 genomes]
rs7962740	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv469359	chr12:39946354-40034699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv558591	chr12:39946354-40034699	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv469361	chr12:39946354-40042220	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv558592	chr12:39946354-40042220	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899014	chr12:39946354-40068896	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv899015	chr12:39946354-40118249	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv899017	chr12:39949147-40081619	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv899018	chr12:39949147-40111761	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv899020	chr12:39985206-40040331	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv899021	chr12:39989172-40053423	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv899022	chr12:40014427-40111761	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40014200-40018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:40015200-40019800	Weak transcription	Brain Germinal Matrix	brain
3	chr12:40015200-40020200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:40015400-40018000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:40015400-40018800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:40015400-40018800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr12:40015400-40019200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr12:40015600-40019000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:40016200-40018200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr12:40016600-40019000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:40016600-40019200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:40016600-40019600	Weak transcription	K562	blood
13	chr12:40016800-40018800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr12:40016800-40019000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr12:40017000-40021600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:40017400-40018800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:40017400-40021600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:40017800-40018000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:40017800-40018000	Enhancers	GM12878-XiMat	blood
20	chr12:40017800-40018200	Enhancers	Primary T cells from cord blood	blood
21	chr12:40017800-40018200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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