Variant report

Variant	rs28636904
Chromosome Location	chr21:47979176-47979177
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	ESRRA	chr21:47979105-47980790	GM12878	blood:	n/a	chr21:47979782-47979792 chr21:47979785-47979797 chr21:47979785-47979795 chr21:47979778-47979791 chr21:47979781-47979797 chr21:47979775-47979791 chr21:47979779-47979789 chr21:47979779-47979791 chr21:47979784-47979797 chr21:47979785-47979795 chr21:47979779-47979789 chr21:47979788-47979798
2	POLR2A	chr21:47979112-47979739	GM12892	blood:	n/a	n/a
3	POLR2A	chr21:47979107-47979931	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:47974804..47979372-chr21:47979836..47984256,6	MCF-7	breast:
2	chr21:47977884..47980372-chr21:47985950..47987706,2	K562	blood:
3	chr21:47976473..47979943-chr21:47981689..47985824,4	K562	blood:
4	chr21:47970600..47973376-chr21:47976429..47979323,2	MCF-7	breast:

Variant related genes	Relation type
DIP2A	TF binding region
ENSG00000160305	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2070431	0.82[ASN][1000 genomes]
rs2226381	0.80[ASN][1000 genomes]
rs2839321	0.85[ASN][1000 genomes]
rs2839365	0.84[ASN][1000 genomes]
rs34529071	0.81[ASN][1000 genomes]
rs34599663	0.83[ASN][1000 genomes]
rs3788266	0.83[ASN][1000 genomes]
rs67935828	0.83[ASN][1000 genomes]
rs8132624	0.80[ASN][1000 genomes]
rs9975257	0.83[ASN][1000 genomes]
rs9978658	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
12	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
13	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
14	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
15	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
16	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
17	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
18	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS 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	30 gene(s)	inside rSNPs	n/a
19	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
20	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
21	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
22	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
23	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
24	nsv1057566	chr21:47915583-48029698	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	n/a
25	nsv587999	chr21:47941916-48103851	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
26	nsv1058589	chr21:47948030-48091343	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
27	nsv1057643	chr21:47953820-48056600	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	n/a
28	nsv544497	chr21:47953820-48056600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS 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 miRNA target site	36 gene(s)	inside rSNPs	n/a
29	nsv914147	chr21:47958657-47982652	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
30	nsv459313	chr21:47964259-47982652	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
31	nsv588000	chr21:47964259-47982652	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
32	nsv588001	chr21:47966504-47986001	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
33	nsv1056734	chr21:47970933-48096945	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
34	esv2760700	chr21:47974055-48054776	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	n/a
35	nsv1062457	chr21:47975809-48096945	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28636904	C21orf56	Cis_1M	lymphoblastoid	RTeQTL
rs28636904	DIP2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47943600-47990600	Strong transcription	Fetal Stomach	stomach
2	chr21:47947600-47989000	Strong transcription	Dnd41	blood
3	chr21:47947600-47991000	Strong transcription	Fetal Muscle Leg	muscle
4	chr21:47948400-47993600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr21:47948600-47993200	Strong transcription	Fetal Intestine Large	intestine
6	chr21:47948800-47979400	Strong transcription	Liver	Liver
7	chr21:47949000-47988200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr21:47949000-47993600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:47949800-47991800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr21:47950000-47989200	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr21:47950000-47991000	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr21:47950200-47993200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr21:47953000-47988200	Strong transcription	Gastric	stomach
14	chr21:47953000-47988600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr21:47953200-47983400	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr21:47953200-47988400	Strong transcription	Fetal Intestine Small	intestine
17	chr21:47953200-47993000	Strong transcription	Osteobl	bone
18	chr21:47953400-47988000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr21:47956200-48001800	Weak transcription	Stomach Mucosa	stomach
20	chr21:47959200-47983400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr21:47960000-47979200	Weak transcription	Right Atrium	heart
22	chr21:47961600-47992800	Strong transcription	Brain Hippocampus Middle	brain
23	chr21:47964600-47988400	Strong transcription	Brain Germinal Matrix	brain
24	chr21:47965200-47991200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr21:47965800-47988600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr21:47965800-47993400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr21:47966200-47993400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:47966400-47987800	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr21:47966600-47988200	Strong transcription	Esophagus	oesophagus
30	chr21:47966800-47985400	Strong transcription	HMEC	breast
31	chr21:47966800-47985800	Weak transcription	K562	blood
32	chr21:47967400-47994800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr21:47968200-47979200	Weak transcription	Psoas Muscle	Psoas
34	chr21:47968600-47990800	Strong transcription	Fetal Brain Female	brain
35	chr21:47969200-47980000	Weak transcription	Fetal Kidney	kidney
36	chr21:47969400-47987600	Strong transcription	Aorta	Aorta
37	chr21:47969600-47979400	Strong transcription	Pancreas	Pancrea
38	chr21:47969600-47988200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr21:47969600-47988400	Strong transcription	Colonic Mucosa	Colon
40	chr21:47969800-47989200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr21:47970200-47992400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr21:47970400-47988200	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr21:47970400-47993200	Strong transcription	Brain Cingulate Gyrus	brain
44	chr21:47971000-47989200	Strong transcription	Placenta	Placenta
45	chr21:47971600-47991600	Strong transcription	Brain Substantia Nigra	brain
46	chr21:47972000-47979200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr21:47972000-47979200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr21:47972000-47988800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr21:47973000-47979400	Strong transcription	Lung	lung
50	chr21:47973200-47993000	Strong transcription	Duodenum Mucosa	Duodenum

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