Variant report

Variant	rs7311546
Chromosome Location	chr12:104614230-104614231
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	MAX	chr12:104613730-104614288	MCF-7	breast:	n/a	n/a
2	TEAD4	chr12:104613797-104614380	MCF-7	breast:	n/a	n/a
3	FOSL2	chr12:104613064-104614287	A549	lung:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
4	MAX	chr12:104612509-104614444	A549	lung:	n/a	n/a
5	TCF12	chr12:104612894-104614304	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr12:104613714-104614240	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr12:104613305-104614240	MCF-7	breast:	n/a	chr12:104613939-104613948 chr12:104613938-104613950 chr12:104613476-104613497 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613492
8	RXRA	chr12:104613069-104614242	SK-N-SH	brain:	n/a	chr12:104614116-104614125 chr12:104613537-104613546 chr12:104613538-104613547
9	SIN3AK20	chr12:104612693-104614243	A549	lung:	n/a	n/a
10	NFIC	chr12:104612662-104614338	SK-N-SH	brain:	n/a	n/a
11	JUND	chr12:104613001-104614298	A549	lung:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613536-104613547 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
12	JUND	chr12:104613186-104614344	MCF-7	breast:	n/a	chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613536-104613547 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
13	FOXA2	chr12:104612941-104614427	A549	lung:	n/a	chr12:104614084-104614096
14	JUND	chr12:104613015-104614234	Hela-S3	cervix:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613536-104613547 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
15	JUN	chr12:104613104-104614255	Hela-S3	cervix:	n/a	chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
16	CEBPB	chr12:104613154-104614296	MCF-7	breast:	n/a	n/a
17	GABPA	chr12:104613149-104614303	MCF-7	breast:	n/a	n/a
18	TCF7L2	chr12:104613213-104614340	MCF-7	breast:	n/a	n/a
19	SIN3AK20	chr12:104613111-104614468	MCF-7	breast:	n/a	n/a
20	GATA3	chr12:104612552-104614331	SK-N-SH	brain:	n/a	chr12:104613939-104613948 chr12:104613938-104613950 chr12:104613476-104613497 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613492
21	EP300	chr12:104613131-104614330	MCF-7	breast:	n/a	chr12:104614147-104614157 chr12:104613965-104613974 chr12:104613538-104613547 chr12:104613537-104613546
22	EP300	chr12:104613020-104614337	T-47D	breast:	n/a	chr12:104614147-104614157 chr12:104613965-104613974 chr12:104613538-104613547 chr12:104613537-104613546
23	BCL3	chr12:104612591-104614327	A549	lung:	n/a	chr12:104613537-104613546 chr12:104613940-104613947 chr12:104613538-104613547
24	JUND	chr12:104612545-104614241	SK-N-SH	brain:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613536-104613547 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
25	SRF	chr12:104612670-104614300	HCT-116	colon:	n/a	n/a
26	ATF3	chr12:104612984-104614344	A549	lung:	n/a	n/a
27	MAX	chr12:104612580-104614325	HCT-116	colon:	n/a	n/a
28	EP300	chr12:104612319-104614606	A549	lung:	n/a	chr12:104614147-104614157 chr12:104613965-104613974 chr12:104613538-104613547 chr12:104613537-104613546
29	FOSL2	chr12:104612540-104614261	SK-N-SH	brain:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
30	SIN3AK20	chr12:104612803-104614362	MCF-7	breast:	n/a	n/a
31	NR2F2	chr12:104613137-104614377	MCF-7	breast:	n/a	n/a
32	EP300	chr12:104613129-104614333	T-47D	breast:	n/a	chr12:104614147-104614157 chr12:104613965-104613974 chr12:104613538-104613547 chr12:104613537-104613546
33	FOSL2	chr12:104613072-104614379	MCF-7	breast:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545
34	HA-E2F1	chr12:104613709-104614574	MCF-7	breast:	n/a	chr12:104614138-104614147
35	TEAD4	chr12:104612911-104614292	A549	lung:	n/a	chr12:104613402-104613411 chr12:104613461-104613470
36	TCF12	chr12:104612668-104615129	A549	lung:	n/a	n/a
37	POLR2A	chr12:104612991-104614266	PANC-1	pancreas:	n/a	n/a
38	ATF3	chr12:104613003-104614277	A549	lung:	n/a	n/a
39	ESR1	chr12:104613767-104614255	T-47D	breast:	n/a	n/a
40	GATA3	chr12:104612528-104614607	A549	lung:	n/a	chr12:104613939-104613948 chr12:104613938-104613950 chr12:104613476-104613497 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613490 chr12:104613483-104613492
41	RAD21	chr12:104612974-104614281	A549	lung:	n/a	n/a
42	CEBPB	chr12:104613025-104614291	Hela-S3	cervix:	n/a	chr12:104613121-104613133
43	FOXM1	chr12:104613143-104614258	ECC-1	luminal epithelium:	n/a	n/a
44	EP300	chr12:104612797-104614287	Hela-S3	cervix:	n/a	chr12:104614147-104614157 chr12:104613965-104613974 chr12:104613538-104613547 chr12:104613537-104613546
45	ZBTB33	chr12:104613046-104614232	A549	lung:	n/a	n/a
46	TCF12	chr12:104612533-104614347	SK-N-SH	brain:	n/a	n/a
47	SP1	chr12:104612572-104614517	A549	lung:	n/a	n/a
48	SIN3AK20	chr12:104612766-104614319	A549	lung:	n/a	n/a
49	PML	chr12:104613722-104614259	MCF-7	breast:	n/a	n/a
50	JUN	chr12:104612946-104614260	K562	blood:	n/a	chr12:104613098-104613107 chr12:104613538-104613546 chr12:104613537-104613546 chr12:104613947-104613959 chr12:104613949-104613957 chr12:104613945-104613956 chr12:104613538-104613547 chr12:104613538-104613545

No.	Distal block	Cell Line	Cell type
1	chr12:104613573..104614403-chr3:184080838..184081389,2	Hela-S3	cervix:
2	chr12:104571693..104572332-chr12:104613947..104614462,2	MCF-7	breast:
3	chr12:104613868..104615389-chr12:104679010..104681119,2	K562	blood:
4	chr12:104611665..104617222-chr12:104678192..104683063,15	MCF-7	breast:
5	chr12:104605545..104609502-chr12:104611890..104614832,4	MCF-7	breast:
6	chr12:104612436..104616572-chr12:104617042..104624166,8	MCF-7	breast:
7	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:
8	chr12:104613560..104615348-chr12:104617225..104620017,2	MCF-7	breast:
9	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000163882	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11111913	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11111921	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111938	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111945	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11536084	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4628754	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964635	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6539125	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7310815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7487242	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7954970	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7966740	0.97[ASN][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	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
2	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
3	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
4	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
5	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104610200-104614800	Weak transcription	Gastric	stomach
2	chr12:104610800-104614800	Weak transcription	Ovary	ovary
3	chr12:104612000-104615400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr12:104612200-104615000	Enhancers	HMEC	breast
5	chr12:104612200-104617400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:104612400-104616400	Enhancers	Placenta	Placenta
7	chr12:104612600-104615000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:104612800-104614400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:104612800-104614400	Enhancers	Fetal Intestine Large	intestine
10	chr12:104612800-104614800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr12:104612800-104615000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr12:104612800-104615000	Enhancers	Fetal Stomach	stomach
13	chr12:104613000-104614400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:104613000-104614600	Enhancers	HepG2	liver
15	chr12:104613000-104615600	Enhancers	Stomach Mucosa	stomach
16	chr12:104613000-104616000	Enhancers	Duodenum Mucosa	Duodenum
17	chr12:104613200-104614400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:104613200-104614400	Active TSS	A549	lung
19	chr12:104613200-104614600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:104613200-104614600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:104613400-104614800	Enhancers	Dnd41	blood
22	chr12:104613600-104615000	Enhancers	Left Ventricle	heart
23	chr12:104613800-104615000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:104614000-104614400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:104614000-104614400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:104614000-104614400	Enhancers	Osteobl	bone
27	chr12:104614000-104614600	Weak transcription	Pancreas	Pancrea
28	chr12:104614000-104614800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:104614000-104614800	Weak transcription	Lung	lung
30	chr12:104614000-104615000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:104614000-104615000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr12:104614000-104615000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:104614000-104615000	Enhancers	NHDF-Ad	bronchial
34	chr12:104614000-104615000	Enhancers	NHEK	skin
35	chr12:104614000-104616000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:104614000-104616000	Weak transcription	Thymus	Thymus
37	chr12:104614000-104617200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:104614000-104617200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:104614000-104617400	Weak transcription	HSMMtube	muscle
40	chr12:104614000-104619600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:104614000-104623400	Weak transcription	Right Atrium	heart
42	chr12:104614200-104614400	Weak transcription	Small Intestine	intestine
43	chr12:104614200-104614600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:104614200-104614600	Enhancers	NH-A	brain
45	chr12:104614200-104614800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:104614200-104614800	Weak transcription	Right Ventricle	heart
47	chr12:104614200-104615800	Enhancers	HUVEC	blood vessel
48	chr12:104614200-104615800	Enhancers	NHLF	lung
49	chr12:104614200-104616000	Enhancers	Hela-S3	cervix
50	chr12:104614200-104616600	Weak transcription	Fetal Lung	lung

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