Variant report

Variant	rs9980169
Chromosome Location	chr21:45664257-45664258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:308)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:308 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr21:45663667-45664476	GM12878	blood:	n/a	n/a
2	POLR2A	chr21:45662969-45664329	GM12891	blood:	n/a	n/a
3	CEBPB	chr21:45663053-45664958	GM12878	blood:	n/a	n/a
4	SMC3	chr21:45663707-45664424	HepG2	liver:	n/a	n/a
5	JUND	chr21:45663654-45664369	MCF-7	breast:	n/a	chr21:45663970-45663981
6	CTCF	chr21:45664078-45664331	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr21:45663689-45664285	HepG2	liver:	n/a	n/a
8	GATA3	chr21:45663492-45664585	MCF-7	breast:	n/a	n/a
9	FOXA2	chr21:45663825-45664273	HepG2	liver:	n/a	n/a
10	MYC	chr21:45664254-45664267	HepG2	liver:	n/a	n/a
11	CTCF	chr21:45664140-45664290	GM12875	blood:	n/a	n/a
12	SIN3A	chr21:45663125-45664391	GM12878	blood:	n/a	n/a
13	PAX5	chr21:45663669-45664365	GM12878	blood:	n/a	n/a
14	CTCF	chr21:45664075-45664327	Hela-S3	cervix:	n/a	n/a
15	BCLAF1	chr21:45662148-45664577	GM12878	blood:	n/a	chr21:45663017-45663026 chr21:45662185-45662194 chr21:45662863-45662876 chr21:45662867-45662880 chr21:45662532-45662545 chr21:45662172-45662185 chr21:45663015-45663028
16	TCF12	chr21:45663455-45664453	MCF-7	breast:	n/a	n/a
17	NR2F2	chr21:45663611-45664430	MCF-7	breast:	n/a	n/a
18	ZNF263	chr21:45663825-45664384	HEK293-T-REx	kidney:	n/a	n/a
19	CTCF	chr21:45664111-45664280	Gliobla	brain:	n/a	n/a
20	BATF	chr21:45663682-45664340	GM12878	blood:	n/a	n/a
21	ZNF143	chr21:45663779-45664269	Hela-S3	cervix:	n/a	n/a
22	EGR1	chr21:45663602-45664481	HCT-116	colon:	n/a	n/a
23	FOSL2	chr21:45663663-45664356	HepG2	liver:	n/a	chr21:45663971-45663982
24	CTCF	chr21:45664120-45664270	HCT-116	colon:	n/a	n/a
25	TBP	chr21:45663229-45664385	GM12878	blood:	n/a	n/a
26	CTCF	chr21:45664120-45664270	GM12864	blood:	n/a	n/a
27	JUN	chr21:45663652-45664645	K562	blood:	n/a	n/a
28	FOSL2	chr21:45663699-45664365	HepG2	liver:	n/a	chr21:45663971-45663982
29	HDAC2	chr21:45663736-45664375	HepG2	liver:	n/a	n/a
30	SIN3AK20	chr21:45663467-45664603	MCF-7	breast:	n/a	n/a
31	CTCF	chr21:45664070-45664325	GM10248	blood:	n/a	n/a
32	CTCF	chr21:45664120-45664270	GM12869	blood:	n/a	n/a
33	KAP1	chr21:45663790-45664333	U2OS	brain:	n/a	chr21:45664300-45664308
34	POLR2A	chr21:45662134-45664429	GM12891	blood:	n/a	n/a
35	POU2F2	chr21:45663651-45664277	GM12878	blood:	n/a	n/a
36	EGR1	chr21:45663671-45664312	MCF-7	breast:	n/a	n/a
37	MAX	chr21:45663622-45664531	HepG2	liver:	n/a	n/a
38	RCOR1	chr21:45663668-45664360	IMR90	lung:	n/a	n/a
39	POLR2A	chr21:45663779-45664283	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr21:45662156-45664538	GM12878	blood:	n/a	n/a
41	CTCF	chr21:45663839-45664377	GM19239	blood:	n/a	n/a
42	WRNIP1	chr21:45663159-45664400	GM12878	blood:	n/a	n/a
43	EGR1	chr21:45663651-45664277	HCT-116	colon:	n/a	n/a
44	MYBL2	chr21:45663722-45664367	HepG2	liver:	n/a	n/a
45	RAD21	chr21:45663715-45664376	GM12878	blood:	n/a	n/a
46	ELF1	chr21:45663704-45664588	GM12878	blood:	n/a	n/a
47	MYBL2	chr21:45663598-45664435	HepG2	liver:	n/a	n/a
48	POLR2A	chr21:45660527-45664598	GM12878	blood:	n/a	n/a
49	STAT5A	chr21:45660864-45664695	GM12878	blood:	n/a	chr21:45662181-45662193 chr21:45661410-45661422 chr21:45663013-45663025 chr21:45663014-45663026
50	ZNF384	chr21:45663721-45664334	GM12878	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45662131..45665488-chr21:45759079..45762763,3	MCF-7	breast:
2	chr21:45622629..45624491-chr21:45663848..45665509,2	MCF-7	breast:
3	chr21:45664074..45664939-chr21:45687442..45688212,2	MCF-7	breast:
4	chr21:45603147..45604698-chr21:45662988..45665089,2	MCF-7	breast:
5	chr21:45661427..45664747-chr21:45681166..45683937,3	MCF-7	breast:
6	chr21:45662446..45664337-chr21:45902333..45904974,2	MCF-7	breast:
7	chr21:45595647..45596418-chr21:45663539..45664451,5	MCF-7	breast:
8	chr21:45588410..45594838-chr21:45658945..45665595,14	MCF-7	breast:
9	chr21:45663550..45664645-chr21:45717261..45718177,3	MCF-7	breast:
10	chr21:45554484..45558321-chr21:45662336..45665430,3	MCF-7	breast:
11	chr21:45658211..45662255-chr21:45662719..45665336,3	K562	blood:
12	chr21:45620311..45631567-chr21:45651002..45670824,52	MCF-7	breast:
13	chr21:45658941..45665769-chr21:45718013..45724632,19	MCF-7	breast:
14	chr21:45663828..45666335-chr21:45687884..45690743,2	MCF-7	breast:
15	chr21:45658347..45670658-chr21:45718073..45723358,28	MCF-7	breast:
16	chr21:45581401..45583188-chr21:45662253..45664319,2	MCF-7	breast:

No data

Variant related genes	Relation type
ICOSLG	TF binding region
ENSG00000232969	Chromatin interaction
ENSG00000142182	Chromatin interaction
ENSG00000160226	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000267913	Chromatin interaction
ENSG00000141959	Chromatin interaction
ENSG00000232124	Chromatin interaction
ENSG00000160223	Chromatin interaction
ENSG00000160221	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2026880	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8129776	0.88[ASN][1000 genomes]
rs9306177	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
9	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
10	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
11	nsv913901	chr21:45615741-45665330	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv913902	chr21:45615741-45709153	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv459295	chr21:45629565-45849864	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
14	nsv587740	chr21:45629565-45849864	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	57 gene(s)	inside rSNPs	diseases
15	nsv913904	chr21:45636881-45700641	Genic enhancers Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv913905	chr21:45640629-45696025	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv913906	chr21:45657970-45818609	Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45661600-45664400	Enhancers	Pancreas	Pancrea
2	chr21:45661600-45664400	Active TSS	Rectal Smooth Muscle	rectum
3	chr21:45661800-45668200	Enhancers	Liver	Liver
4	chr21:45662000-45665000	Enhancers	Stomach Mucosa	stomach
5	chr21:45662200-45664400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr21:45662400-45664800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr21:45662400-45665400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr21:45662600-45664400	Bivalent Enhancer	Fetal Thymus	thymus
9	chr21:45662600-45664400	Enhancers	Gastric	stomach
10	chr21:45662800-45664400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr21:45662800-45664600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr21:45662800-45664600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr21:45662800-45667800	Weak transcription	Brain Anterior Caudate	brain
14	chr21:45662800-45705600	Weak transcription	Right Atrium	heart
15	chr21:45663000-45664600	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr21:45663200-45664400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr21:45663200-45664600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr21:45663200-45664600	Enhancers	HSMMtube	muscle
19	chr21:45663200-45665800	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr21:45663200-45666000	Flanking Active TSS	GM12878-XiMat	blood
21	chr21:45663400-45664400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr21:45663400-45664400	Flanking Active TSS	Hela-S3	cervix
23	chr21:45663400-45666200	Enhancers	Primary hematopoietic stem cells	blood
24	chr21:45663600-45664400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr21:45663600-45664400	Bivalent Enhancer	HSMM	muscle
26	chr21:45663600-45664400	Bivalent Enhancer	HUVEC	blood vessel
27	chr21:45663600-45664600	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr21:45663600-45664600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr21:45663600-45664600	Enhancers	Colonic Mucosa	Colon
30	chr21:45663600-45665000	Enhancers	Fetal Intestine Small	intestine
31	chr21:45663600-45670400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr21:45663800-45664600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
33	chr21:45663800-45664600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
34	chr21:45663800-45664800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr21:45663800-45665000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr21:45663800-45668400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr21:45663800-45668400	Enhancers	HepG2	liver
38	chr21:45663800-45669600	Enhancers	Fetal Intestine Large	intestine
39	chr21:45664000-45664600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
40	chr21:45664000-45664600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr21:45664000-45664600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr21:45664000-45664600	Enhancers	Duodenum Mucosa	Duodenum
43	chr21:45664000-45664600	Bivalent Enhancer	Thymus	Thymus
44	chr21:45664000-45665400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr21:45664000-45665600	Enhancers	Primary T cells from cord blood	blood
46	chr21:45664000-45665800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr21:45664000-45665800	Enhancers	Spleen	Spleen
48	chr21:45664000-45666200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr21:45664000-45667800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr21:45664000-45671800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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