Variant report

Variant	rs28801979
Chromosome Location	chr21:47607088-47607089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:47607086-47607715	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr21:47605590-47608104	HepG2	liver:	n/a	n/a
3	POLR2A	chr21:47607054-47608226	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47571793..47574970-chr21:47606794..47610224,4	MCF-7	breast:
2	chr21:47606790..47609628-chr21:47614415..47615920,2	MCF-7	breast:
3	chr21:47605676..47611866-chr21:47647121..47650700,5	K562	blood:
4	chr21:47601884..47606848-chr21:47606938..47611467,11	MCF-7	breast:
5	chr21:47606363..47609230-chr21:47646261..47649400,3	MCF-7	breast:

No data

Variant related genes	Relation type
SPATC1L	TF binding region
ENSG00000228404	Chromatin interaction
ENSG00000215424	Chromatin interaction
ENSG00000160284	Chromatin interaction
ENSG00000160285	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12329662	0.85[EUR][1000 genomes]
rs12329665	0.85[EUR][1000 genomes]
rs12329667	0.85[EUR][1000 genomes]
rs12329859	0.85[EUR][1000 genomes]
rs12329865	0.83[GIH][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs16978977	0.82[MKK][hapmap]
rs16979001	1.00[CEU][hapmap]
rs16979014	1.00[CEU][hapmap]
rs16979053	0.80[MKK][hapmap]
rs17176940	1.00[ASN][1000 genomes]
rs17182531	1.00[ASN][1000 genomes]
rs17182753	1.00[ASN][1000 genomes]
rs17182990	1.00[ASN][1000 genomes]
rs17183213	1.00[ASN][1000 genomes]
rs17183382	1.00[ASN][1000 genomes]
rs2254522	0.83[LWK][hapmap]
rs2298693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28560443	0.80[EUR][1000 genomes]
rs35785446	0.85[EUR][1000 genomes]
rs55774624	0.83[ASN][1000 genomes]
rs7280396	0.85[EUR][1000 genomes]
rs7281813	0.85[EUR][1000 genomes]
rs7281816	0.81[MKK][hapmap]
rs8127105	1.00[CEU][hapmap]
rs8128293	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8129484	0.82[EUR][1000 genomes]
rs8131130	0.85[EUR][1000 genomes]
rs8134875	1.00[CEU][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs9975914	0.90[EUR][1000 genomes]
rs9977392	0.85[EUR][1000 genomes]
rs9980665	0.85[EUR][1000 genomes]
rs9981713	0.85[EUR][1000 genomes]
rs9981777	0.85[EUR][1000 genomes]
rs9983895	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
2	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
4	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
6	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
8	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
9	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
10	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
11	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
12	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
13	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
14	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
15	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
16	nsv914098	chr21:47467894-47619784	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
17	nsv1061087	chr21:47476088-47643219	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
18	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
19	nsv914101	chr21:47491014-47650362	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
20	nsv914108	chr21:47514885-47609677	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
21	nsv914115	chr21:47526240-47614469	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
22	nsv914116	chr21:47535248-47650362	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
23	nsv914128	chr21:47558994-47609677	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
24	nsv914129	chr21:47566828-47609677	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
25	nsv914131	chr21:47572244-47609677	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
26	nsv914132	chr21:47572244-47619784	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
27	nsv914133	chr21:47583506-47613486	Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
28	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
29	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
30	esv1822235	chr21:47588465-47610305	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
31	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS 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	85 gene(s)	inside rSNPs	n/a
32	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47604600-47609000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr21:47605000-47607200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr21:47605000-47607800	Weak transcription	Liver	Liver
4	chr21:47605000-47608400	Weak transcription	Pancreas	Pancrea
5	chr21:47605000-47608600	Weak transcription	Gastric	stomach
6	chr21:47605000-47609200	Weak transcription	Lung	lung
7	chr21:47605000-47609200	Weak transcription	Spleen	Spleen
8	chr21:47605000-47609400	Weak transcription	Aorta	Aorta
9	chr21:47605000-47609400	Weak transcription	Esophagus	oesophagus
10	chr21:47605000-47610600	Weak transcription	Colon Smooth Muscle	Colon
11	chr21:47605000-47611600	Weak transcription	Small Intestine	intestine
12	chr21:47605000-47613600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr21:47605000-47613600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr21:47605000-47633200	Weak transcription	Stomach Mucosa	stomach
15	chr21:47605200-47607200	Weak transcription	Left Ventricle	heart
16	chr21:47605200-47607200	Weak transcription	Right Atrium	heart
17	chr21:47605200-47607600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr21:47605200-47607600	Weak transcription	Brain Germinal Matrix	brain
19	chr21:47605200-47607800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr21:47605200-47607800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr21:47605200-47608000	Weak transcription	HepG2	liver
22	chr21:47605200-47608000	Weak transcription	NH-A	brain
23	chr21:47605200-47608200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr21:47605200-47608200	Weak transcription	HSMM	muscle
25	chr21:47605200-47608400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr21:47605200-47608400	Weak transcription	Dnd41	blood
27	chr21:47605200-47608400	Weak transcription	Osteobl	bone
28	chr21:47605200-47609200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr21:47605200-47609400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr21:47605200-47609400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr21:47605200-47609400	Weak transcription	Colonic Mucosa	Colon
32	chr21:47605200-47610800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr21:47605200-47613200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr21:47605200-47646200	Weak transcription	Psoas Muscle	Psoas
35	chr21:47605400-47607400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr21:47605400-47607400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr21:47605400-47607400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr21:47605400-47607400	Weak transcription	Fetal Stomach	stomach
39	chr21:47605400-47607600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr21:47605400-47607600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr21:47605400-47607600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr21:47605400-47607600	Weak transcription	Brain Substantia Nigra	brain
43	chr21:47605400-47607600	Weak transcription	NHDF-Ad	bronchial
44	chr21:47605400-47607600	Weak transcription	NHEK	skin
45	chr21:47605400-47607800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr21:47605400-47607800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr21:47605400-47607800	Weak transcription	Adipose Nuclei	Adipose
48	chr21:47605400-47608000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr21:47605400-47608000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr21:47605400-47608000	Weak transcription	Hela-S3	cervix

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