Variant report

Variant	rs28431406
Chromosome Location	chr21:45078476-45078477
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr21:45078430-45078636	HepG2	liver:	n/a	chr21:45078500-45078520 chr21:45078503-45078517 chr21:45078502-45078518
2	POLR2A	chr21:45078261-45080594	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr21:45078403-45078580	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr21:45078235-45080098	K562	blood:	n/a	n/a
5	SETDB1	chr21:45078329-45079773	K562	blood:	n/a	chr21:45078646-45078655 chr21:45079306-45079315
6	JUN	chr21:45078290-45080288	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:45078437-45078487	CMK	blood:	n/a
2	chr21:45078437-45078487	A549	lung:	n/a
3	chr21:45078437-45078487	H1-hESC	embryonic stem cell:	embryo
4	chr21:45078437-45078487	MCF10A-Er-Src	breast:	n/a
5	chr21:45078437-45078487	HPAEpiC	pulmonary alveolar:	n/a
6	chr21:45078437-45078487	AG04449	skin:	fetal
7	chr21:45078437-45078487	HRE	kidney:	n/a
8	chr21:45078437-45078487	Jurkat	blood:	n/a
9	chr21:45078437-45078487	U87	brain:	n/a
10	chr21:45078437-45078487	HRCEpiC	kidney:	n/a
11	chr21:45078437-45078487	SK-N-SH_RA	brain:	n/a
12	chr21:45078437-45078487	SKMC	muscle:	n/a
13	chr21:45078437-45078487	HepG2	liver:	n/a
14	chr21:45078437-45078487	Caco-2	colon:	n/a
15	chr21:45078437-45078487	HAEpiC	amniotic membrane:	n/a
16	chr21:45078437-45078487	HMEC	breast:	n/a
17	chr21:45078437-45078487	HCPEpiC	choroid plexus:	n/a
18	chr21:45078437-45078487	ovcar-3	ovarian:	n/a
19	chr21:45078437-45078487	Hepatocyte	liver:	n/a
20	chr21:45078437-45078487	SK-N-SH	brain:	n/a
21	chr21:45078437-45078487	NHDF-neo	bronchial:	n/a
22	chr21:45078437-45078487	GM12878	blood:	n/a
23	chr21:45078437-45078487	NHBE	bronchial:	n/a
24	chr21:45078437-45078487	HEK293	kidney:	embryo
25	chr21:45078437-45078487	GM19239	blood:	n/a
26	chr21:45078437-45078487	HCF	heart:	n/a
27	chr21:45078437-45078487	IMR90	lung:	fetal
28	chr21:45078437-45078487	GM12892	blood:	n/a
29	chr21:45078437-45078487	PFSK-1	brain:	n/a
30	chr21:45078437-45078487	HIPEpiC	eye:	n/a
31	chr21:45078437-45078487	SK-N-MC	brain:	n/a
32	chr21:45078437-45078487	AoSMC	blood vessel:	n/a
33	chr21:45078437-45078487	PANC-1	pancreas:	n/a
34	chr21:45078437-45078487	HUVEC	blood vessel:	n/a
35	chr21:45078437-45078487	PrEC	prostate:	n/a
36	chr21:45078437-45078487	ProgFib	skin:	n/a
37	chr21:45078437-45078487	Hela-S3	cervix:	n/a
38	chr21:45078437-45078487	LNCaP	prostate:	n/a
39	chr21:45078437-45078487	MCF-7	breast:	n/a
40	chr21:45078437-45078487	AG09319	gingival:	n/a
41	chr21:45078437-45078487	NB4	blood:	n/a
42	chr21:45078437-45078487	HNPCEpiC	eye:	n/a
43	chr21:45078437-45078487	HRPEpiC	eye:	n/a
44	chr21:45078437-45078487	NH-A	brain:	n/a
45	chr21:45078437-45078487	BJ	skin:	n/a
46	chr21:45078437-45078487	AG04450	lung:	fetal
47	chr21:45078437-45078487	HCT-116	colon:	n/a
48	chr21:45078437-45078487	AG09309	skin:	n/a
49	chr21:45078437-45078487	HL-60	blood:	n/a
50	chr21:45078437-45078487	BE2_C	brain:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45076259..45080839-chr21:45207005..45211007,4	MCF-7	breast:
2	chr21:45077838..45080620-chr21:45152184..45154376,2	MCF-7	breast:
3	chr21:45077301..45079668-chr21:45138843..45140832,3	K562	blood:
4	chr21:45077768..45080499-chr21:45194775..45197148,2	MCF-7	breast:
5	chr21:45078168..45080813-chr21:45138258..45142239,4	K562	blood:
6	chr21:45077264..45080546-chr21:45137817..45144125,9	MCF-7	breast:
7	chr10:30721466..30724212-chr21:45078300..45080802,2	MCF-7	breast:
8	chr21:44845531..44848527-chr21:45078395..45081083,3	K562	blood:
9	chr21:45077212..45079990-chr21:45193841..45196934,5	MCF-7	breast:
10	chr21:44297552..44300422-chr21:45078415..45081013,3	K562	blood:
11	chr21:44526256..44528655-chr21:45076981..45079726,2	MCF-7	breast:

No data

Variant related genes	Relation type
HSF2BP	TF binding region
RRP1B	TF binding region
RRP1B	CpG island
HSF2BP	CpG island
ENSG00000160194	Chromatin interaction
ENSG00000107968	Chromatin interaction
ENSG00000160201	Chromatin interaction
ENSG00000160213	Chromatin interaction
ENSG00000160209	Chromatin interaction
ENSG00000160193	Chromatin interaction
ENSG00000160214	Chromatin interaction
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10427514	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10483077	0.83[AMR][1000 genomes]
rs10483078	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11089090	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11908919	0.83[AMR][1000 genomes]
rs11909195	0.83[AMR][1000 genomes]
rs11909530	0.83[AMR][1000 genomes]
rs11909813	0.83[AMR][1000 genomes]
rs11909916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11911293	0.91[AMR][1000 genomes]
rs11911735	0.83[AMR][1000 genomes]
rs11911856	0.83[AMR][1000 genomes]
rs17004507	0.83[AMR][1000 genomes]
rs17004581	0.83[AMR][1000 genomes]
rs17004585	0.83[AMR][1000 genomes]
rs17004586	0.83[AMR][1000 genomes]
rs17004587	0.83[AMR][1000 genomes]
rs17004589	0.83[AMR][1000 genomes]
rs17004590	0.83[AMR][1000 genomes]
rs17004592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004593	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004595	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28782771	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28852206	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7510543	0.83[AMR][1000 genomes]
rs9917493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834106	chr21:44992387-45109489	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	15 gene(s)	inside rSNPs	diseases
3	nsv587700	chr21:45007956-45095200	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv913874	chr21:45041790-45191005	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active 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	36 gene(s)	inside rSNPs	diseases
5	nsv531544	chr21:45071371-45202912	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45060400-45078600	Weak transcription	Pancreas	Pancrea
2	chr21:45065800-45078600	Weak transcription	Fetal Muscle Leg	muscle
3	chr21:45066600-45078800	Weak transcription	Brain Hippocampus Middle	brain
4	chr21:45066600-45078800	Weak transcription	Right Atrium	heart
5	chr21:45066600-45079000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:45066600-45079000	Weak transcription	Brain Substantia Nigra	brain
7	chr21:45066800-45078800	Weak transcription	Fetal Intestine Small	intestine
8	chr21:45067000-45078600	Weak transcription	HepG2	liver
9	chr21:45074000-45078800	Weak transcription	K562	blood
10	chr21:45074800-45079400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:45075200-45079000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr21:45075200-45079000	Weak transcription	A549	lung
13	chr21:45075400-45078800	Weak transcription	Osteobl	bone
14	chr21:45075600-45078600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr21:45075600-45078800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr21:45075600-45078800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr21:45075600-45078800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr21:45075600-45078800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr21:45075600-45078800	Weak transcription	Liver	Liver
20	chr21:45075600-45078800	Weak transcription	Hela-S3	cervix
21	chr21:45075800-45078600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr21:45075800-45079000	Weak transcription	NH-A	brain
23	chr21:45075800-45079000	Weak transcription	NHDF-Ad	bronchial
24	chr21:45076000-45078800	Weak transcription	HMEC	breast
25	chr21:45076000-45078800	Weak transcription	NHEK	skin
26	chr21:45076600-45079000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr21:45076800-45078600	Enhancers	Placenta	Placenta
28	chr21:45076800-45079000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr21:45076800-45079000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr21:45077000-45078800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr21:45077200-45079000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr21:45077200-45079000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr21:45077400-45078800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr21:45077400-45079000	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr21:45077400-45079000	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr21:45077400-45079000	Enhancers	Fetal Thymus	thymus
37	chr21:45077400-45079200	Enhancers	Spleen	Spleen
38	chr21:45077400-45079400	Enhancers	Primary hematopoietic stem cells	blood
39	chr21:45077600-45078600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr21:45077600-45078800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr21:45077600-45078800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr21:45077600-45079000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr21:45077600-45079000	Enhancers	Primary B cells from cord blood	blood
44	chr21:45077600-45079000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr21:45077600-45079000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr21:45077600-45079000	Enhancers	Fetal Brain Male	brain
47	chr21:45077600-45079000	Enhancers	Right Ventricle	heart
48	chr21:45077600-45079200	Enhancers	Lung	lung
49	chr21:45077800-45078600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr21:45077800-45078600	Weak transcription	Thymus	Thymus

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