Variant report

Variant	rs73956461
Chromosome Location	chr2:111554491-111554492
allele	G/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	GATA3	chr2:111554088-111554709	MCF-7	breast:	n/a	chr2:111554306-111554322
2	GATA3	chr2:111554347-111554726	MCF-7	breast:	n/a	n/a
3	GATA3	chr2:111554360-111554741	MCF-7	breast:	n/a	n/a
4	GATA3	chr2:111554201-111554871	MCF-7	breast:	n/a	chr2:111554306-111554322
5	FOXA1	chr2:111554235-111554726	T-47D	breast:	n/a	n/a
6	EP300	chr2:111554320-111554757	T-47D	breast:	n/a	n/a
7	GATA3	chr2:111554224-111554774	T-47D	breast:	n/a	chr2:111554306-111554322
8	NR2F2	chr2:111554237-111554807	MCF-7	breast:	n/a	n/a
9	HDAC2	chr2:111554236-111554779	MCF-7	breast:	n/a	n/a
10	CTCF	chr2:111554480-111554630	MCF-7	breast:	n/a	n/a
11	REST	chr2:111554450-111554862	MCF-7	breast:	n/a	chr2:111554647-111554667 chr2:111554647-111554667
12	CEBPB	chr2:111554266-111554734	MCF-7	breast:	n/a	chr2:111554385-111554396
13	JUND	chr2:111554203-111554789	T-47D	breast:	n/a	n/a
14	GATA3	chr2:111554211-111554772	T-47D	breast:	n/a	chr2:111554306-111554322
15	FOXA1	chr2:111554229-111554693	T-47D	breast:	n/a	n/a
16	EP300	chr2:111554342-111554747	T-47D	breast:	n/a	n/a
17	SIN3AK20	chr2:111554148-111554878	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111547409..111550001-chr2:111554228..111556468,2	MCF-7	breast:

Variant related genes	Relation type
ACOXL	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs55693530	0.86[AFR][1000 genomes]
rs56238232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57166069	0.86[AFR][1000 genomes]
rs57934984	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58287229	1.00[AMR][1000 genomes]
rs58796451	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59952084	0.86[AFR][1000 genomes]
rs72832840	0.84[AFR][1000 genomes]
rs73954652	1.00[AMR][1000 genomes]
rs73954653	1.00[AMR][1000 genomes]
rs73954660	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73954672	0.86[AFR][1000 genomes]
rs73956432	0.86[AFR][1000 genomes]
rs73956436	0.90[AFR][1000 genomes]
rs73956438	0.86[AFR][1000 genomes]
rs73956442	1.00[AMR][1000 genomes]
rs73956443	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956445	1.00[AMR][1000 genomes]
rs73956446	1.00[AMR][1000 genomes]
rs73956448	1.00[AMR][1000 genomes]
rs73956449	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956450	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956451	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956453	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956454	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956455	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956457	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956458	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956459	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956462	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956463	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956467	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1008758	chr2:111415136-111626467	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv535890	chr2:111415136-111626467	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv997829	chr2:111486961-111780537	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111531200-111566200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:111531600-111556800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:111531600-111558600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:111551200-111555000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:111552200-111555400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:111552200-111556000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:111552400-111556200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:111552400-111557800	Weak transcription	Fetal Heart	heart
9	chr2:111552600-111567400	Weak transcription	Right Ventricle	heart
10	chr2:111552800-111556200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:111553000-111555600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:111553000-111556400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:111553200-111554800	Enhancers	Fetal Lung	lung
14	chr2:111553200-111556600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:111553400-111555400	Enhancers	Fetal Muscle Leg	muscle
16	chr2:111553400-111558200	Weak transcription	Left Ventricle	heart
17	chr2:111553800-111554800	Enhancers	Fetal Stomach	stomach
18	chr2:111554000-111554800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:111554000-111554800	Enhancers	Pancreas	Pancrea
20	chr2:111554000-111554800	Enhancers	Right Atrium	heart
21	chr2:111554200-111554800	Enhancers	Placenta	Placenta
22	chr2:111554400-111554800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr2:111554400-111555200	Weak transcription	Fetal Brain Male	brain

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