Variant report

Variant	rs16857586
Chromosome Location	chr2:11672343-11672344
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:11672190-11673087	MCF-7	breast:	n/a	n/a
2	TCF7L2	chr2:11672321-11673069	MCF-7	breast:	n/a	n/a
3	FOXM1	chr2:11672210-11673148	MCF-7	breast:	n/a	n/a
4	JUND	chr2:11672197-11673102	MCF-7	breast:	n/a	chr2:11672713-11672724
5	ESR1	chr2:11672260-11673082	T-47D	breast:	n/a	chr2:11672657-11672674 chr2:11672658-11672673 chr2:11672658-11672675
6	RAD21	chr2:11672212-11673074	MCF-7	breast:	n/a	n/a
7	JUND	chr2:11672262-11673060	MCF-7	breast:	n/a	chr2:11672713-11672724
8	HA-E2F1	chr2:11672330-11673029	MCF-7	breast:	n/a	n/a
9	ESR1	chr2:11672214-11673068	T-47D	breast:	n/a	chr2:11672657-11672674 chr2:11672658-11672673 chr2:11672658-11672675
10	NR2F2	chr2:11672212-11673081	MCF-7	breast:	n/a	n/a
11	SIN3AK20	chr2:11672130-11673196	MCF-7	breast:	n/a	n/a
12	FOSL2	chr2:11672307-11673086	MCF-7	breast:	n/a	n/a
13	POLR2A	chr2:11670574-11673676	MCF-7	breast:	n/a	n/a
14	ESR1	chr2:11672310-11673068	T-47D	breast:	n/a	chr2:11672657-11672674 chr2:11672658-11672673 chr2:11672658-11672675
15	FOXM1	chr2:11672292-11673221	MCF-7	breast:	n/a	n/a
16	EP300	chr2:11672248-11673224	MCF-7	breast:	n/a	n/a
17	GATA3	chr2:11672338-11673005	MCF-7	breast:	n/a	n/a
18	ZNF217	chr2:11672296-11673509	MCF-7	breast:	n/a	n/a
19	GATA3	chr2:11672241-11674316	MCF-7	breast:	n/a	chr2:11673809-11673817
20	SIN3AK20	chr2:11672190-11673246	MCF-7	breast:	n/a	n/a
21	GATA3	chr2:11672091-11673296	MCF-7	breast:	n/a	chr2:11672136-11672147
22	EP300	chr2:11672160-11673215	MCF-7	breast:	n/a	chr2:11672189-11672203
23	HDAC2	chr2:11672302-11673091	MCF-7	breast:	n/a	chr2:11672479-11672493
24	MAX	chr2:11672290-11673163	MCF-7	breast:	n/a	n/a
25	SRF	chr2:11672279-11673148	MCF-7	breast:	n/a	n/a
26	FOSL2	chr2:11672341-11673064	MCF-7	breast:	n/a	n/a
27	TCF12	chr2:11672179-11673072	MCF-7	breast:	n/a	n/a
28	NR2F2	chr2:11672301-11673084	MCF-7	breast:	n/a	n/a
29	TCF12	chr2:11672085-11673264	MCF-7	breast:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11664576..11665195-chr2:11672161..11672758,2	MCF-7	breast:
2	chr2:11638395..11639328-chr2:11672080..11673402,33	MCF-7	breast:
3	chr2:11670272..11672993-chr20:52308680..52310728,2	MCF-7	breast:
4	chr2:11671059..11672742-chr2:20270351..20272377,2	MCF-7	breast:
5	chr2:11671718..11674128-chr5:176738557..176740122,2	MCF-7	breast:
6	chr2:11652567..11653314-chr2:11672197..11673097,3	MCF-7	breast:
7	chr12:52586456..52588653-chr2:11670748..11673207,2	MCF-7	breast:
8	chr2:11272147..11274930-chr2:11671339..11675156,3	MCF-7	breast:
9	chr2:11671144..11672993-chr2:11680123..11682594,2	K562	blood:
10	chr2:11670047..11672634-chr6:32937032..32938585,2	MCF-7	breast:
11	chr2:11643423..11644238-chr2:11672221..11673048,2	MCF-7	breast:
12	chr2:11671380..11672993-chr2:11681094..11683884,2	K562	blood:
13	chr2:11638381..11639354-chr2:11672110..11673685,53	MCF-7	breast:
14	chr2:11638351..11639377-chr2:11672093..11673435,81	MCF-7	breast:
15	chr2:11670481..11672921-chr2:11803900..11805580,2	MCF-7	breast:
16	chr2:11670570..11676286-chr2:11818745..11824828,7	MCF-7	breast:
17	chr2:11670624..11672438-chr20:52740971..52743291,2	MCF-7	breast:
18	chr2:11652567..11653117-chr2:11672197..11673095,3	MCF-7	breast:
19	chr2:11671599..11673261-chr3:170586531..170588800,2	MCF-7	breast:
20	chr2:11671004..11673308-chr2:20648459..20650037,2	MCF-7	breast:
21	chr2:11638425..11639482-chr2:11672224..11673064,4	MCF-7	breast:
22	chr2:11638082..11639401-chr2:11671985..11673160,9	MCF-7	breast:
23	chr2:11671113..11672841-chr2:11917292..11919829,2	MCF-7	breast:
24	chr2:11669797..11672713-chr6:27100529..27102950,2	MCF-7	breast:

No data

Variant related genes	Relation type
GREB1	TF binding region
ENSG00000228496	Chromatin interaction
ENSG00000213347	Chromatin interaction
ENSG00000163584	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000145063	Chromatin interaction
ENSG00000150873	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000134324	Chromatin interaction
ENSG00000264010	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13388093	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2043542	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs4668729	1.00[CEU][hapmap]
rs59489734	0.96[AFR][1000 genomes]
rs59885883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60215345	0.82[AFR][1000 genomes]
rs6719003	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6719009	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6728365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73189353	0.83[AFR][1000 genomes]
rs73189377	0.96[AFR][1000 genomes]
rs7566661	1.00[CEU][hapmap]

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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11656200-11672800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:11664600-11676200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:11665000-11678000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:11666200-11672400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:11666600-11672400	Weak transcription	Brain Angular Gyrus	brain
6	chr2:11667400-11674600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:11667800-11672600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:11669400-11678000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:11670400-11675800	Enhancers	HepG2	liver
10	chr2:11671200-11676800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:11671200-11679600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:11671400-11672400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:11671400-11672400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:11671400-11672400	Weak transcription	Pancreas	Pancrea
15	chr2:11671400-11672400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:11671400-11672600	Weak transcription	Brain Substantia Nigra	brain
17	chr2:11671400-11674600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:11671400-11674600	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:11671400-11674600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:11671400-11679200	Weak transcription	Right Atrium	heart
21	chr2:11671600-11675000	Weak transcription	Psoas Muscle	Psoas
22	chr2:11671800-11672400	Enhancers	Hela-S3	cervix
23	chr2:11672000-11672400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:11672000-11672400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr2:11672000-11672800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:11672200-11672400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:11672200-11672400	Enhancers	HMEC	breast
28	chr2:11672200-11672400	Enhancers	NHEK	skin
29	chr2:11672200-11672600	Enhancers	Osteobl	bone
30	chr2:11672200-11672800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:11672200-11672800	Active TSS	Ovary	ovary
32	chr2:11672200-11673000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr2:11672200-11673000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:11672200-11674400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:11672200-11674600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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