Variant report

Variant	rs72967859
Chromosome Location	chr3:53699038-53699039
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr3:53698865-53699222	T-47D	breast:	n/a	n/a
2	ESR1	chr3:53698786-53699282	T-47D	breast:	n/a	n/a
3	ESR1	chr3:53698858-53699169	T-47D	breast:	n/a	n/a
4	TCF7L2	chr3:53698884-53699343	MCF-7	breast:	n/a	n/a
5	TCF12	chr3:53698575-53699540	MCF-7	breast:	n/a	n/a
6	TEAD4	chr3:53698879-53699238	MCF-7	breast:	n/a	n/a
7	ZNF217	chr3:53698808-53699392	MCF-7	breast:	n/a	n/a
8	NR2F2	chr3:53698823-53699386	MCF-7	breast:	n/a	n/a
9	FOXM1	chr3:53698821-53699263	MCF-7	breast:	n/a	n/a
10	GATA3	chr3:53698982-53699182	SH-SY5Y	brain:	n/a	n/a
11	FOXA1	chr3:53698775-53699238	T-47D	breast:	n/a	n/a
12	HA-E2F1	chr3:53698790-53699318	MCF-7	breast:	n/a	n/a
13	GATA2	chr3:53698829-53699196	SH-SY5Y	brain:	n/a	n/a
14	GATA3	chr3:53698790-53699295	T-47D	breast:	n/a	n/a
15	GATA3	chr3:53698860-53699273	T-47D	breast:	n/a	n/a
16	EP300	chr3:53698721-53699378	T-47D	breast:	n/a	n/a
17	EP300	chr3:53698719-53699282	MCF-7	breast:	n/a	n/a
18	HDAC2	chr3:53698736-53699129	MCF-7	breast:	n/a	n/a
19	GATA3	chr3:53698659-53699396	MCF-7	breast:	n/a	n/a
20	SIN3AK20	chr3:53698603-53699421	MCF-7	breast:	n/a	n/a
21	FOXA1	chr3:53698803-53699239	T-47D	breast:	n/a	n/a
22	GATA3	chr3:53698789-53699297	MCF-7	breast:	n/a	n/a
23	ESR1	chr3:53698805-53699272	T-47D	breast:	n/a	n/a
24	HDAC2	chr3:53698762-53699271	MCF-7	breast:	n/a	n/a
25	EP300	chr3:53698866-53699328	T-47D	breast:	n/a	n/a
26	MAX	chr3:53698863-53699237	MCF-7	breast:	n/a	n/a
27	MYC	chr3:53698943-53699173	MCF-7	breast:	n/a	n/a
28	ESR1	chr3:53698844-53699202	T-47D	breast:	n/a	n/a
29	NR2F2	chr3:53698797-53699482	MCF-7	breast:	n/a	n/a
30	GATA3	chr3:53698565-53699563	MCF-7	breast:	n/a	n/a
31	GATA3	chr3:53698819-53699247	MCF-7	breast:	n/a	n/a
32	EP300	chr3:53698836-53699234	MCF-7	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53698054..53699675-chr3:53742176..53745087,2	MCF-7	breast:
2	chr3:53584684..53586821-chr3:53697849..53700213,2	MCF-7	breast:
3	chr3:53584946..53585871-chr3:53698734..53699592,4	MCF-7	breast:

No data

Variant related genes	Relation type
CACNA1D	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs17053285	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17053295	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292918	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2612020	0.86[ASN][1000 genomes]
rs2633708	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2633709	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2680657	0.86[ASN][1000 genomes]
rs2680659	0.86[ASN][1000 genomes]
rs33970402	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36003262	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774459	1.00[EUR][1000 genomes]
rs3774484	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774485	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774499	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774500	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774513	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3774521	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774524	0.95[ASN][1000 genomes]
rs55641883	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55881044	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55999888	0.84[ASN][1000 genomes]
rs58036565	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58236730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6765947	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6788419	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs715781	1.00[EUR][1000 genomes]
rs72967878	1.00[AMR][1000 genomes]
rs72978521	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72978524	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72978526	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72978528	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72978531	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72978534	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72978536	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73840122	1.00[EUR][1000 genomes]
rs73842064	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7633188	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs898412	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs898413	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs898414	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311511	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9848595	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53677600-53700000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:53689600-53707400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:53692000-53707600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:53694200-53699200	Strong transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:53694200-53700400	Strong transcription	Fetal Intestine Large	intestine
7	chr3:53694400-53701000	Weak transcription	Fetal Kidney	kidney
8	chr3:53696000-53700200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:53696800-53706600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:53697600-53702400	Weak transcription	Liver	Liver
11	chr3:53698000-53714000	Weak transcription	Brain Substantia Nigra	brain
12	chr3:53698600-53700000	Weak transcription	Fetal Lung	lung
13	chr3:53698800-53711200	Weak transcription	Spleen	Spleen
14	chr3:53699000-53700200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:53699000-53700200	Weak transcription	Fetal Intestine Small	intestine

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