Variant report

Variant	rs28375993
Chromosome Location	chr21:40177054-40177055
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	CTCF	chr21:40176921-40177262	A549	lung:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
2	MAX	chr21:40176897-40178012	ECC-1	luminal epithelium:	n/a	chr21:40177454-40177463 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
3	MXI1	chr21:40176328-40180482	SK-N-SH	brain:	n/a	chr21:40176631-40176646 chr21:40176633-40176648
4	CTCF	chr21:40176980-40177130	MCF-7	breast:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
5	CTCF	chr21:40177020-40177170	Hela-S3	cervix:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
6	SMC3	chr21:40177041-40177246	GM12878	blood:	n/a	chr21:40177094-40177108
7	MAX	chr21:40176914-40178092	SK-N-SH	brain:	n/a	chr21:40177454-40177463 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
8	GTF2F1	chr21:40176834-40178025	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr21:40175826-40184443	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr21:40176800-40178471	NB4	blood:	n/a	chr21:40177454-40177463 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
11	RAD21	chr21:40176849-40177397	H1-hESC	embryonic stem cell:	n/a	chr21:40177096-40177109 chr21:40177093-40177112
12	RAD21	chr21:40176494-40178046	ECC-1	luminal epithelium:	n/a	chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178030-40178044
13	CTCF	chr21:40177020-40177170	AG09319	gingival:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
14	TCF7L2	chr21:40176617-40177947	Hela-S3	cervix:	n/a	n/a
15	ZNF384	chr21:40177020-40177876	K562	blood:	n/a	n/a
16	CTCF	chr21:40176960-40177110	GM12878	blood:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
17	USF2	chr21:40176599-40177107	Hela-S3	cervix:	n/a	chr21:40176808-40176819
18	CTCF	chr21:40176989-40177215	Spleen_OC	spleen:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
19	CTCF	chr21:40176960-40177110	HFF-Myc	foreskin:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
20	CTCF	chr21:40177020-40177170	WERI-Rb-1	eye:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
21	POLR2A	chr21:40176831-40178983	HL-60	blood:	n/a	n/a
22	CTCF	chr21:40177040-40177190	Hela-S3	cervix:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
23	CTCF	chr21:40177000-40177150	GM12875	blood:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
24	CTCF	chr21:40176949-40177226	MCF-7	breast:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
25	CTCF	chr21:40176980-40177130	BJ	skin:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
26	EP300	chr21:40176364-40180305	SK-N-SH	brain:	n/a	chr21:40179345-40179359 chr21:40177988-40177997 chr21:40178219-40178228 chr21:40179343-40179357 chr21:40178259-40178275 chr21:40179344-40179358 chr21:40178028-40178044 chr21:40179342-40179356 chr21:40178328-40178344 chr21:40178322-40178331
27	CCNT2	chr21:40176993-40179135	K562	blood:	n/a	n/a
28	CTCF	chr21:40177020-40177170	RPTEC	kidney:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
29	TCF12	chr21:40176681-40178155	A549	lung:	n/a	n/a
30	CTCF	chr21:40176980-40177130	GM12873	blood:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
31	CTCF	chr21:40176961-40177226	Pancreas_OC	pancreas:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
32	TBL1XR1	chr21:40176988-40177899	K562	blood:	n/a	n/a
33	CREB1	chr21:40176932-40177240	A549	lung:	n/a	n/a
34	ZKSCAN1	chr21:40176931-40177978	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr21:40176818-40178228	HUVEC	blood vessel:	n/a	n/a
36	CTCF	chr21:40176960-40177227	K562	blood:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
37	CTCF	chr21:40177040-40177190	BE2_C	brain:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
38	CTCF	chr21:40176980-40177130	HEK293	kidney:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
39	REST	chr21:40176846-40177593	U87	brain:	n/a	chr21:40177144-40177162
40	CTCF	chr21:40177040-40177190	HRE	kidney:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
41	POLR2A	chr21:40177052-40178113	PFSK-1	brain:	n/a	n/a
42	RAD21	chr21:40176426-40178698	MCF-7	breast:	n/a	chr21:40178543-40178556 chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178101-40178114 chr21:40178124-40178136 chr21:40178030-40178044
43	ZBTB7A	chr21:40176963-40177197	K562	blood:	n/a	n/a
44	CTCF	chr21:40176982-40177213	GM19240	blood:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
45	CTCF	chr21:40176951-40177226	NHEK	skin:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
46	CTCF	chr21:40176980-40177130	GM12872	blood:	n/a	chr21:40177095-40177108 chr21:40177092-40177110
47	SIN3AK20	chr21:40176999-40178059	SK-N-SH	brain:	n/a	n/a
48	E2F6	chr21:40176650-40178180	K562	blood:	n/a	chr21:40177209-40177226 chr21:40178104-40178114 chr21:40177212-40177223
49	BACH1	chr21:40177000-40177993	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr21:40176941-40177249	MCF-7	breast:	n/a	chr21:40177095-40177108 chr21:40177092-40177110

No.	Distal block	Cell Line	Cell type
1	chr21:40176403..40178101-chr21:40218059..40219647,2	K562	blood:
2	chr21:40175328..40180167-chr21:40553641..40558387,7	K562	blood:
3	chr21:40105514..40106081-chr21:40176310..40177112,2	MCF-7	breast:
4	chr21:40175328..40178574-chr21:40554098..40556223,3	K562	blood:
5	chr21:40176416..40179104-chr21:40257484..40260730,3	MCF-7	breast:
6	chr21:40176632..40177186-chr21:40455915..40456479,2	MCF-7	breast:
7	chr21:40176662..40177180-chr21:40510094..40510804,2	MCF-7	breast:
8	chr21:40176601..40179515-chr21:40218059..40219886,2	K562	blood:
9	chr21:40174647..40179577-chr21:40285247..40287797,5	MCF-7	breast:
10	chr21:40176740..40177648-chr7:16685493..16686292,2	Hela-S3	cervix:
11	chr1:210546726..210547661-chr21:40176943..40177887,2	Hela-S3	cervix:
12	chr21:40176416..40178956-chr21:40498284..40502065,4	MCF-7	breast:
13	chr21:40176263..40179138-chr21:40817088..40818717,2	K562	blood:

Variant related genes	Relation type
ETS2	TF binding region
ENSG00000272991	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000228861	Chromatin interaction
ENSG00000234035	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000136261	Chromatin interaction
ENSG00000229986	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000229925	Chromatin interaction
ENSG00000183527	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11911369	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57740627	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60328145	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs714780	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73450548	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73450552	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8128181	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8133056	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8133164	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8134019	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8134441	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058591	chr21:40114130-40190594	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv3430408	chr21:40176482-40179580	Enhancers Active TSS Weak transcription Flanking 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	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40172600-40177200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr21:40175400-40177200	Enhancers	Lung	lung
3	chr21:40176000-40177400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr21:40176000-40177600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr21:40176200-40177400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr21:40176400-40177200	Enhancers	Fetal Heart	heart
7	chr21:40176400-40177400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr21:40176400-40177400	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr21:40176400-40177400	Flanking Active TSS	Fetal Intestine Small	intestine
10	chr21:40176400-40177400	Flanking Active TSS	NH-A	brain
11	chr21:40176400-40177600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr21:40176400-40177600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr21:40176600-40177200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr21:40176600-40177200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr21:40176600-40177400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr21:40176600-40177400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr21:40176600-40177400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr21:40176600-40177400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr21:40176600-40177400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr21:40176600-40177400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr21:40176600-40177400	Flanking Active TSS	Fetal Intestine Large	intestine
22	chr21:40176600-40177400	Flanking Active TSS	Fetal Lung	lung
23	chr21:40176600-40177600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr21:40176600-40177600	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr21:40176600-40177600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr21:40176600-40177600	Flanking Active TSS	Dnd41	blood
27	chr21:40176600-40177600	Flanking Active TSS	Osteobl	bone
28	chr21:40176600-40179800	Active TSS	Rectal Smooth Muscle	rectum
29	chr21:40176600-40180400	Active TSS	Ovary	ovary
30	chr21:40176600-40181600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr21:40176600-40182000	Active TSS	Brain Anterior Caudate	brain
32	chr21:40176800-40177200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr21:40176800-40177200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr21:40176800-40177200	Active TSS	Colonic Mucosa	Colon
35	chr21:40176800-40177200	Flanking Active TSS	NHDF-Ad	bronchial
36	chr21:40176800-40177400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr21:40176800-40177400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr21:40176800-40177400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr21:40176800-40177400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr21:40176800-40177400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr21:40176800-40177400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr21:40176800-40177400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
43	chr21:40176800-40177400	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr21:40176800-40177400	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr21:40176800-40177400	Flanking Active TSS	Placenta	Placenta
46	chr21:40176800-40177400	Flanking Active TSS	Fetal Stomach	stomach
47	chr21:40176800-40177400	Flanking Active TSS	Fetal Thymus	thymus
48	chr21:40176800-40177400	Flanking Active TSS	Pancreas	Pancrea
49	chr21:40176800-40177400	Flanking Active TSS	HUVEC	blood vessel
50	chr21:40176800-40177400	Flanking Active TSS	K562	blood

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