Variant report

Variant	rs3859679
Chromosome Location	chr21:15436475-15436476
allele	A/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	POLR2A	chr21:15436221-15436810	IMR90	lung:	n/a	n/a
2	POLR2A	chr21:15436286-15436499	Hela-S3	cervix:	n/a	n/a
3	HEY1	chr21:15436299-15436507	K562	blood:	n/a	chr21:15436341-15436356
4	MYC	chr21:15435893-15436891	MCF-7	breast:	n/a	chr21:15436870-15436880
5	ELF1	chr21:15436026-15436913	MCF-7	breast:	n/a	chr21:15436326-15436335 chr21:15436858-15436870 chr21:15436560-15436572 chr21:15436325-15436336 chr21:15436339-15436351
6	POLR2A	chr21:15436192-15436528	PANC-1	pancreas:	n/a	n/a
7	MYC	chr21:15436026-15436877	MCF-7	breast:	n/a	n/a
8	HA-E2F1	chr21:15436001-15436976	MCF-7	breast:	n/a	chr21:15436562-15436571 chr21:15436271-15436281
9	TAF1	chr21:15436275-15436495	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr21:15436053-15436938	MCF-7	breast:	n/a	n/a
11	POLR2A	chr21:15436047-15436655	ProgFib	skin:	n/a	n/a
12	MXI1	chr21:15435964-15436513	IMR90	lung:	n/a	n/a
13	HEY1	chr21:15436269-15436497	K562	blood:	n/a	chr21:15436341-15436356
14	POLR2A	chr21:15436224-15436490	GM12878	blood:	n/a	n/a
15	MAX	chr21:15436109-15436881	MCF-7	breast:	n/a	chr21:15436870-15436880
16	POLR2A	chr21:15436202-15436509	GM12892	blood:	n/a	n/a
17	POLR2A	chr21:15436112-15436525	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr21:15435961-15436981	MCF-7	breast:	n/a	n/a
19	ELF1	chr21:15435975-15436884	MCF-7	breast:	n/a	chr21:15436326-15436335 chr21:15436858-15436870 chr21:15436560-15436572 chr21:15436325-15436336 chr21:15436339-15436351
20	POLR2A	chr21:15436014-15436894	MCF-7	breast:	n/a	n/a
21	MAX	chr21:15436447-15436909	MCF-7	breast:	n/a	chr21:15436870-15436880
22	POLR2A	chr21:15436273-15436500	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ANKRD20A18P	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12626293	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2187066	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2822389	0.93[ASN][1000 genomes]
rs2822391	0.93[ASN][1000 genomes]
rs2822394	0.90[ASN][1000 genomes]
rs4816915	0.93[ASN][1000 genomes]
rs4816917	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61082953	0.83[ASN][1000 genomes]
rs7276301	0.90[ASN][1000 genomes]
rs7281893	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9981819	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9984987	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058202	chr21:14706767-15628668	Weak transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1067433	chr21:14736298-15507502	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1055396	chr21:14756514-15507502	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv1062639	chr21:14775729-15507502	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
5	nsv587015	chr21:14957973-15448560	Genic enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1058072	chr21:15372509-15568171	Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1056787	chr21:15407504-15530291	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv964485	chr21:15431964-15437845	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a
9	nsv979524	chr21:15431964-15441809	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	n/a
10	esv3358889	chr21:15434106-15436654	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15401800-15452000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr21:15402600-15442400	Weak transcription	Dnd41	blood
3	chr21:15423000-15442200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr21:15423400-15455600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr21:15423600-15443000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr21:15425800-15443400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:15428800-15449000	Weak transcription	Fetal Lung	lung
8	chr21:15430400-15442400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr21:15433000-15442200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr21:15433000-15442400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr21:15434000-15437600	ZNF genes & repeats	Fetal Brain Female	brain
12	chr21:15434600-15437000	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr21:15435400-15436600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:15435600-15436800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:15435600-15436800	ZNF genes & repeats	Fetal Stomach	stomach
16	chr21:15435800-15436800	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr21:15435800-15437200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr21:15435800-15438400	Active TSS	Esophagus	oesophagus
19	chr21:15436000-15436800	Active TSS	NHLF	lung
20	chr21:15436000-15437000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr21:15436000-15437000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr21:15436000-15437000	Active TSS	Brain Anterior Caudate	brain
23	chr21:15436000-15437000	Active TSS	Brain Cingulate Gyrus	brain
24	chr21:15436000-15437000	Active TSS	Left Ventricle	heart
25	chr21:15436000-15437000	Active TSS	Right Atrium	heart
26	chr21:15436000-15437000	Active TSS	NH-A	brain
27	chr21:15436000-15437200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr21:15436000-15437200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr21:15436000-15437400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr21:15436000-15437400	Active TSS	Stomach Smooth Muscle	stomach
31	chr21:15436000-15437600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr21:15436200-15437000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:15436200-15437000	Active TSS	Aorta	Aorta
34	chr21:15436200-15437000	Active TSS	Brain Angular Gyrus	brain
35	chr21:15436200-15437000	Active TSS	Brain Hippocampus Middle	brain
36	chr21:15436200-15437000	Active TSS	Pancreas	Pancrea
37	chr21:15436400-15436800	Active TSS	Gastric	stomach
38	chr21:15436400-15437000	Active TSS	Primary hematopoietic stem cells	blood
39	chr21:15436400-15437000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr21:15436400-15439000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr21:15436400-15442400	Weak transcription	Thymus	Thymus

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