Variant report

Variant	rs9976897
Chromosome Location	chr21:46238885-46238886
allele	A/G
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	chr21:46237813-46238892	HL-60	blood:	n/a	n/a
2	POLR2A	chr21:46237200-46240136	K562	blood:	n/a	n/a
3	YY1	chr21:46238471-46238979	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr21:46236589-46239537	GM12878	blood:	n/a	n/a
5	POLR2A	chr21:46236858-46238968	GM12892	blood:	n/a	n/a
6	POLR2A	chr21:46237439-46238935	NB4	blood:	n/a	n/a
7	HCFC1	chr21:46237336-46238913	K562	blood:	n/a	n/a
8	E2F6	chr21:46238547-46238952	H1-hESC	embryonic stem cell:	n/a	chr21:46238730-46238742 chr21:46238734-46238741 chr21:46238734-46238741 chr21:46238734-46238741
9	POLR2A	chr21:46236599-46239893	K562	blood:	n/a	n/a
10	POLR2A	chr21:46237226-46239099	PBDE	blood:	n/a	n/a
11	POLR2A	chr21:46236952-46238898	MCF-7	breast:	n/a	n/a
12	POLR2A	chr21:46238850-46238945	MCF-7	breast:	n/a	n/a
13	SETDB1	chr21:46238001-46240087	K562	blood:	n/a	chr21:46239232-46239256
14	POLR2A	chr21:46236874-46239052	GM12878	blood:	n/a	n/a
15	CCNT2	chr21:46237381-46238923	K562	blood:	n/a	n/a
16	POLR2A	chr21:46237296-46239463	K562	blood:	n/a	n/a
17	MAX	chr21:46237824-46238914	H1-hESC	embryonic stem cell:	n/a	chr21:46238032-46238045 chr21:46238298-46238308 chr21:46238123-46238132 chr21:46238805-46238815 chr21:46238034-46238043 chr21:46238034-46238043 chr21:46238033-46238044
18	HMGN3	chr21:46237204-46238924	K562	blood:	n/a	n/a
19	POLR2A	chr21:46237390-46239171	K562	blood:	n/a	n/a
20	E2F6	chr21:46237797-46239120	H1-hESC	embryonic stem cell:	n/a	chr21:46238730-46238742 chr21:46238734-46238741 chr21:46238477-46238487 chr21:46238734-46238741 chr21:46237956-46237971 chr21:46238734-46238741
21	POLR2A	chr21:46237474-46238974	GM12878	blood:	n/a	n/a
22	POLR2A	chr21:46237347-46238900	GM18526	blood:	n/a	n/a
23	HEY1	chr21:46238848-46239721	K562	blood:	n/a	n/a
24	MXI1	chr21:46237212-46238908	IMR90	lung:	n/a	chr21:46238033-46238042
25	JUN	chr21:46237275-46239002	K562	blood:	n/a	chr21:46237471-46237478 chr21:46238469-46238478 chr21:46238229-46238238 chr21:46237471-46237479 chr21:46237471-46237479
26	POLR2A	chr21:46236149-46239701	GM12878	blood:	n/a	n/a
27	POLR2A	chr21:46236937-46240089	HepG2	liver:	n/a	n/a
28	POLR2A	chr21:46236230-46240188	K562	blood:	n/a	n/a
29	CBX3	chr21:46238761-46239209	K562	blood:	n/a	n/a
30	POLR2A	chr21:46237245-46238898	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:50092081..50093923-chr21:46237222..46239021,2	MCF-7	breast:
2	chr21:46231216..46239677-chr21:46289090..46295542,14	K562	blood:
3	chr21:46232702..46239829-chr21:46289967..46296620,21	MCF-7	breast:
4	chr21:46231904..46241990-chr21:46492035..46500735,28	K562	blood:
5	chr21:46235954..46239342-chr21:46346367..46350296,5	K562	blood:
6	chr21:46235459..46240790-chr21:46329963..46334235,7	MCF-7	breast:
7	chr21:45298008..45300010-chr21:46238849..46240379,2	K562	blood:
8	chr21:46236678..46239215-chr21:46284689..46286960,3	MCF-7	breast:
9	chr21:46235517..46239255-chr21:46289829..46295572,6	K562	blood:
10	chr21:46235651..46239241-chr21:46493223..46495632,4	MCF-7	breast:
11	chr21:46231789..46243695-chr21:46286819..46295664,23	MCF-7	breast:
12	chr21:46233435..46239577-chr21:46329843..46334353,8	MCF-7	breast:
13	chr21:46234752..46239628-chr21:46345760..46349592,8	MCF-7	breast:
14	chr21:46234824..46239565-chr21:46284858..46289652,5	K562	blood:
15	chr21:46238172..46240580-chr21:46333314..46335686,2	K562	blood:
16	chr21:46236285..46239693-chr21:46357237..46360614,5	K562	blood:
17	chr21:46235785..46239443-chr21:46357143..46362674,8	MCF-7	breast:
18	chr21:46236918..46239386-chr21:46357793..46361272,3	K562	blood:
19	chr17:56708448..56710403-chr21:46237510..46239366,2	MCF-7	breast:
20	chr21:46231513..46241255-chr21:46492035..46497390,26	K562	blood:
21	chr1:45285250..45286056-chr21:46238038..46238888,2	Hela-S3	cervix:

Variant related genes	Relation type
SUMO3	TF binding region
ENSG00000183255	Chromatin interaction
ENSG00000142546	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs8131092	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9980203	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv459298	chr21:46223847-46277968	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv587813	chr21:46223847-46277968	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv913963	chr21:46223847-46277968	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv913966	chr21:46229393-46261390	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
13	esv3345023	chr21:46236474-46239372	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
14	esv3410893	chr21:46236549-46239397	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46236600-46239000	Active TSS	Hela-S3	cervix
2	chr21:46236800-46239000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr21:46236800-46239000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:46236800-46239000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr21:46236800-46239000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr21:46237000-46239000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr21:46237200-46239000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:46237200-46239000	Active TSS	NHEK	skin
9	chr21:46237400-46239000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr21:46237400-46239000	Active TSS	Duodenum Mucosa	Duodenum
11	chr21:46237600-46239000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr21:46237600-46239000	Active TSS	Fetal Brain Female	brain
13	chr21:46237600-46239000	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr21:46238200-46239000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr21:46238200-46239000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr21:46238200-46239000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr21:46238200-46239000	Enhancers	Fetal Brain Male	brain
18	chr21:46238200-46239000	Flanking Active TSS	Spleen	Spleen
19	chr21:46238400-46239000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr21:46238400-46239000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr21:46238400-46239000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr21:46238400-46239000	Flanking Active TSS	Pancreas	Pancrea
23	chr21:46238400-46239200	ZNF genes & repeats	Fetal Intestine Large	intestine
24	chr21:46238400-46239400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr21:46238400-46239400	Flanking Active TSS	Dnd41	blood
26	chr21:46238600-46239000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr21:46238600-46239000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr21:46238600-46239000	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr21:46238600-46239000	Flanking Active TSS	Right Ventricle	heart
30	chr21:46238600-46239200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr21:46238600-46239200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr21:46238600-46239200	Flanking Active TSS	HepG2	liver
33	chr21:46238600-46239200	Flanking Active TSS	K562	blood
34	chr21:46238600-46239200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr21:46238600-46239400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr21:46238600-46239800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr21:46238600-46240200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr21:46238800-46239000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
39	chr21:46238800-46239000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr21:46238800-46239000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr21:46238800-46239000	Enhancers	Primary T cells from cord blood	blood
42	chr21:46238800-46239000	Enhancers	Primary T cells fromperipheralblood	blood
43	chr21:46238800-46239000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr21:46238800-46239000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr21:46238800-46239000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr21:46238800-46239000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr21:46238800-46239000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr21:46238800-46239000	Active TSS	Colonic Mucosa	Colon
49	chr21:46238800-46239000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
50	chr21:46238800-46239000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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