Variant report

Variant	rs56172552
Chromosome Location	chr21:16435028-16435029
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	CTCF	chr21:16435000-16435150	HCPEpiC	choroid plexus:	n/a	chr21:16435071-16435092
2	CTCF	chr21:16434980-16435130	NHDF-neo	bronchial:	n/a	chr21:16435071-16435092
3	ZNF143	chr21:16434988-16435274	GM12878	blood:	n/a	n/a
4	MYC	chr21:16434186-16435332	K562	blood:	n/a	n/a
5	BHLHE40	chr21:16434968-16435218	GM12878	blood:	n/a	n/a
6	CTCF	chr21:16434945-16435219	Spleen_OC	spleen:	n/a	chr21:16435071-16435092
7	CTCF	chr21:16434920-16435070	HUVEC	blood vessel:	n/a	n/a
8	CTCF	chr21:16435000-16435150	AG09319	gingival:	n/a	chr21:16435071-16435092
9	CTCF	chr21:16435000-16435150	HPAF	blood vessel:	n/a	chr21:16435071-16435092
10	CTCF	chr21:16434980-16435130	MCF-7	breast:	n/a	chr21:16435071-16435092
11	CTCF	chr21:16434980-16435130	GM12878	blood:	n/a	chr21:16435071-16435092
12	RAD21	chr21:16434958-16435226	SK-N-SH_RA	brain:	n/a	chr21:16435070-16435089
13	CTCF	chr21:16434960-16435110	GM06990	blood:	n/a	chr21:16435071-16435092
14	CTCF	chr21:16435026-16435128	LNCaP	prostate:	n/a	chr21:16435071-16435092
15	CTCF	chr21:16435020-16435170	AoAF	blood vessel:	n/a	chr21:16435071-16435092
16	TBL1XR1	chr21:16434408-16435291	K562	blood:	n/a	n/a
17	CTCF	chr21:16434940-16435090	HCFaa	heart:	n/a	n/a
18	CTCF	chr21:16434960-16435110	HEEpiC	esophagus:	n/a	chr21:16435071-16435092
19	CTCF	chr21:16435000-16435150	HVMF	connective:	n/a	chr21:16435071-16435092
20	CTCF	chr21:16434920-16435070	BJ	skin:	n/a	n/a
21	CTCF	chr21:16435000-16435150	GM12866	blood:	n/a	chr21:16435071-16435092
22	EP300	chr21:16434988-16435393	GM12878	blood:	n/a	n/a
23	CTCF	chr21:16435020-16435170	HRPEpiC	eye:	n/a	chr21:16435071-16435092
24	CTCF	chr21:16434980-16435130	AoAF	blood vessel:	n/a	chr21:16435071-16435092
25	POLR2A	chr21:16434884-16435074	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr21:16435016-16435117	K562	blood:	n/a	chr21:16435071-16435092
27	CTCF	chr21:16434920-16435070	Caco-2	colon:	n/a	n/a
28	POLR2A	chr21:16433055-16438919	MCF-7	breast:	n/a	n/a
29	TBP	chr21:16435013-16435404	GM12878	blood:	n/a	n/a
30	CTCF	chr21:16435020-16435170	HBMEC	blood vessel:	n/a	chr21:16435071-16435092
31	CTCF	chr21:16434898-16435257	GM12878	blood:	n/a	chr21:16435071-16435092
32	RAD21	chr21:16434936-16435175	GM12878	blood:	n/a	chr21:16435070-16435089
33	CTCF	chr21:16434975-16435151	Medullo	brain:	n/a	chr21:16435071-16435092
34	POLR2A	chr21:16434972-16435172	MCF10A-Er-Src	breast:	n/a	n/a
35	CTCF	chr21:16434960-16435110	HMF	breast:	n/a	chr21:16435071-16435092
36	CTCF	chr21:16434940-16435090	AG09319	gingival:	n/a	n/a
37	RAD21	chr21:16434876-16435309	Hela-S3	cervix:	n/a	chr21:16435070-16435089
38	RAD21	chr21:16434946-16435247	GM12878	blood:	n/a	chr21:16435070-16435089
39	POLR2A	chr21:16434935-16435291	U87	brain:	n/a	n/a
40	FOS	chr21:16434963-16435119	MCF10A-Er-Src	breast:	n/a	n/a
41	CTCF	chr21:16434960-16435110	AG10803	skin:	n/a	chr21:16435071-16435092
42	CTCF	chr21:16435008-16435121	Pancreas_OC	pancreas:	n/a	chr21:16435071-16435092
43	RAD21	chr21:16434795-16435344	MCF-7	breast:	n/a	chr21:16435070-16435089
44	RAD21	chr21:16434900-16435297	HepG2	liver:	n/a	chr21:16435070-16435089
45	CTCF	chr21:16435000-16435150	SAEC	small airway:	n/a	chr21:16435071-16435092
46	CTCF	chr21:16434969-16435170	HUVEC	blood vessel:	n/a	chr21:16435071-16435092
47	CTCF	chr21:16434980-16435130	HPF	lung:	n/a	chr21:16435071-16435092
48	CTCF	chr21:16434980-16435130	AG10803	skin:	n/a	chr21:16435071-16435092
49	CTCF	chr21:16435020-16435170	AG04449	skin:	n/a	chr21:16435071-16435092
50	GATA1	chr21:16434176-16435653	PBDE	blood:	n/a	chr21:16434233-16434245 chr21:16434235-16434242

No.	Distal block	Cell Line	Cell type
1	chr21:16245453..16248261-chr21:16433985..16435650,2	MCF-7	breast:
2	chr21:16434967..16437063-chr21:16711446..16713527,2	MCF-7	breast:
3	chr21:16379403..16381413-chr21:16433127..16435083,2	MCF-7	breast:
4	chr21:16356082..16358745-chr21:16434038..16436986,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236471	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2823127	1.00[EUR][1000 genomes]
rs56314547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7275597	1.00[EUR][1000 genomes]
rs7279936	1.00[EUR][1000 genomes]
rs73891935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73895207	1.00[AMR][1000 genomes]
rs9975362	1.00[EUR][1000 genomes]
rs9976439	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060151	chr21:16295713-16435497	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv544378	chr21:16295713-16435497	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv834048	chr21:16324481-16489570	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv587050	chr21:16413682-16462268	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1059303	chr21:16423727-16466112	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv544379	chr21:16423727-16466112	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16422800-16435200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr21:16423600-16435200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:16423800-16435200	Weak transcription	Fetal Brain Male	brain
4	chr21:16424400-16435400	Weak transcription	Gastric	stomach
5	chr21:16427600-16435200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr21:16428400-16435200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr21:16428800-16435200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr21:16429000-16439200	Active TSS	A549	lung
9	chr21:16429800-16435200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr21:16430000-16435200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr21:16430000-16435400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr21:16430000-16435400	Weak transcription	Pancreas	Pancrea
13	chr21:16430000-16436000	Weak transcription	Aorta	Aorta
14	chr21:16430000-16436000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr21:16430200-16435400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr21:16430400-16435400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr21:16431400-16435400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:16431600-16435200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr21:16432000-16435200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr21:16432400-16435600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr21:16432600-16436000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr21:16432800-16435200	Enhancers	Brain Angular Gyrus	brain
23	chr21:16432800-16435400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr21:16432800-16435400	Enhancers	Primary B cells from peripheral blood	blood
25	chr21:16432800-16435400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr21:16432800-16439000	Active TSS	GM12878-XiMat	blood
27	chr21:16433000-16435200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr21:16433000-16435200	Enhancers	Fetal Lung	lung
29	chr21:16433000-16435200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr21:16433000-16435600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr21:16433000-16435800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr21:16433000-16439200	Active TSS	Right Atrium	heart
33	chr21:16433200-16435200	Enhancers	Hela-S3	cervix
34	chr21:16433200-16435200	Flanking Active TSS	Osteobl	bone
35	chr21:16433400-16435400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr21:16433400-16439000	Active TSS	Psoas Muscle	Psoas
37	chr21:16433600-16435200	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr21:16433600-16435800	Flanking Active TSS	HUVEC	blood vessel
39	chr21:16433600-16436000	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr21:16433600-16436200	Flanking Active TSS	Dnd41	blood
41	chr21:16433800-16435200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr21:16433800-16435400	Weak transcription	Left Ventricle	heart
43	chr21:16433800-16435400	Weak transcription	Small Intestine	intestine
44	chr21:16433800-16435600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr21:16433800-16436200	Weak transcription	Spleen	Spleen
46	chr21:16433800-16439000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr21:16433800-16439000	Active TSS	HSMM	muscle
48	chr21:16434200-16435200	Enhancers	Fetal Brain Female	brain
49	chr21:16434200-16435200	Flanking Active TSS	NH-A	brain
50	chr21:16434200-16435200	Flanking Active TSS	NHEK	skin

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