Variant report

Variant	rs73392593
Chromosome Location	chr12:104607980-104607981
allele	A/G
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	REST	chr12:104607545-104608145	A549	lung:	n/a	n/a
2	EP300	chr12:104607630-104608104	T-47D	breast:	n/a	n/a
3	SIN3AK20	chr12:104607763-104608107	PFSK-1	brain:	n/a	n/a
4	REST	chr12:104607638-104608121	PFSK-1	brain:	n/a	n/a
5	GATA3	chr12:104607705-104608229	SK-N-SH	brain:	n/a	n/a
6	FOSL2	chr12:104607718-104608254	SK-N-SH	brain:	n/a	n/a
7	EP300	chr12:104607550-104608143	A549	lung:	n/a	n/a
8	FOXA2	chr12:104607486-104608174	A549	lung:	n/a	chr12:104607741-104607753 chr12:104607761-104607773
9	EP300	chr12:104607719-104608272	SK-N-SH_RA	brain:	n/a	n/a
10	PBX3	chr12:104607649-104608216	SK-N-SH	brain:	n/a	n/a
11	RCOR1	chr12:104607564-104608232	IMR90	lung:	n/a	n/a
12	PBX3	chr12:104607698-104608339	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr12:104607648-104608413	SK-N-SH	brain:	n/a	n/a
14	FOXA1	chr12:104607702-104608014	T-47D	breast:	n/a	chr12:104607741-104607753 chr12:104607761-104607773
15	MYC	chr12:104607820-104608075	MCF10A-Er-Src	breast:	n/a	n/a
16	TCF7L2	chr12:104607701-104608185	PANC-1	pancreas:	n/a	n/a
17	RAD21	chr12:104607732-104608090	SK-N-SH_RA	brain:	n/a	n/a
18	POLR2A	chr12:104607656-104608212	SK-N-SH	brain:	n/a	n/a
19	TCF12	chr12:104607409-104608582	A549	lung:	n/a	chr12:104608377-104608387
20	ESR1	chr12:104607703-104607988	T-47D	breast:	n/a	n/a
21	GATA3	chr12:104607552-104608198	A549	lung:	n/a	n/a
22	EP300	chr12:104607628-104608286	SK-N-SH	brain:	n/a	n/a
23	RAD21	chr12:104607727-104608100	SK-N-SH_RA	brain:	n/a	n/a
24	TCF12	chr12:104607532-104608483	SK-N-SH	brain:	n/a	chr12:104608377-104608387
25	POLR2A	chr12:104607712-104608039	U87	brain:	n/a	n/a
26	GATA3	chr12:104607943-104608132	SH-SY5Y	brain:	n/a	n/a
27	MAX	chr12:104607741-104608140	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr12:104607579-104608308	PFSK-1	brain:	n/a	n/a
29	GATA2	chr12:104607907-104608080	SH-SY5Y	brain:	n/a	n/a
30	REST	chr12:104607675-104608078	PFSK-1	brain:	n/a	n/a
31	FOSL2	chr12:104607558-104608362	A549	lung:	n/a	n/a
32	SP1	chr12:104607564-104608334	A549	lung:	n/a	n/a
33	SP1	chr12:104607540-104608232	A549	lung:	n/a	n/a
34	EP300	chr12:104607734-104608242	SK-N-SH_RA	brain:	n/a	n/a
35	TEAD4	chr12:104607710-104608325	SK-N-SH	brain:	n/a	n/a
36	GATA3	chr12:104607642-104608130	T-47D	breast:	n/a	n/a
37	ESR1	chr12:104607614-104608002	T-47D	breast:	n/a	n/a
38	SIN3AK20	chr12:104607726-104608024	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr12:104607749-104608142	SK-N-SH	brain:	n/a	n/a
40	NFIC	chr12:104607662-104608326	SK-N-SH	brain:	n/a	n/a
41	REST	chr12:104607775-104607998	SK-N-SH	brain:	n/a	n/a
42	FOXA1	chr12:104607546-104608017	T-47D	breast:	n/a	chr12:104607741-104607753 chr12:104607761-104607773
43	ESR1	chr12:104607644-104608057	T-47D	breast:	n/a	n/a
44	POLR2A	chr12:104607603-104608153	PANC-1	pancreas:	n/a	n/a
45	FOS	chr12:104607782-104608052	MCF10A-Er-Src	breast:	n/a	n/a
46	REST	chr12:104607739-104608037	PANC-1	pancreas:	n/a	n/a
47	MAX	chr12:104607727-104608159	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr12:104607561-104608156	PANC-1	pancreas:	n/a	n/a
49	JUND	chr12:104607663-104608119	A549	lung:	n/a	n/a
50	FOXA2	chr12:104607493-104608080	A549	lung:	n/a	chr12:104607741-104607753 chr12:104607761-104607773

No.	Distal block	Cell Line	Cell type
1	chr12:104605545..104609502-chr12:104611890..104614832,4	MCF-7	breast:
2	chr12:104606650..104611349-chr12:104679680..104683932,8	K562	blood:
3	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:
4	chr12:104606513..104608916-chr12:104687474..104689999,2	K562	blood:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10400561	0.83[AFR][1000 genomes]
rs11111931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11111946	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12296767	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12308914	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12310731	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12311576	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12314235	0.86[EUR][1000 genomes]
rs12322184	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12322245	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17035297	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57554346	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59871203	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61524019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73392581	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73392582	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73392588	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73394507	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73394524	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73394536	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104599200-104609200	Weak transcription	Ovary	ovary
2	chr12:104602000-104609200	Weak transcription	HSMM	muscle
3	chr12:104607000-104609200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:104607800-104608000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr12:104607800-104608000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:104607800-104608000	Enhancers	NH-A	brain
7	chr12:104607800-104608200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:104607800-104608400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:104607800-104608400	Enhancers	Hela-S3	cervix
10	chr12:104607800-104608400	Enhancers	HUVEC	blood vessel
11	chr12:104607800-104608400	Enhancers	NHLF	lung
12	chr12:104607800-104608600	Flanking Active TSS	A549	lung
13	chr12:104607800-104609200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:104607800-104609200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:104607800-104609200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:104607800-104609200	Enhancers	Osteobl	bone
17	chr12:104607800-104609400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:104607800-104609400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:104607800-104609800	Enhancers	NHDF-Ad	bronchial

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