Variant report

Variant	rs28375937
Chromosome Location	chr21:46288454-46288455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
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	PBX3	chr21:46288323-46288533	GM12878	blood:	n/a	n/a
2	POLR2A	chr21:46288169-46288457	HepG2	liver:	n/a	n/a
3	NFYB	chr21:46288276-46288647	GM12878	blood:	n/a	n/a
4	WRNIP1	chr21:46288405-46288617	GM12878	blood:	n/a	n/a
5	YY1	chr21:46288235-46288480	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:46288440-46288898	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46249596..46252365-chr21:46286693..46288889,2	K562	blood:
2	chr21:46288400..46294755-chr21:46304910..46312238,10	K562	blood:
3	chr21:46288437..46290185-chr21:46399908..46402286,2	MCF-7	breast:
4	chr21:46272684..46279612-chr21:46286573..46290125,9	K562	blood:
5	chr21:46234824..46239565-chr21:46284858..46289652,5	K562	blood:
6	chr21:46247392..46250185-chr21:46286804..46289409,3	MCF-7	breast:
7	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
8	chr21:46231789..46243695-chr21:46286819..46295664,23	MCF-7	breast:
9	chr21:46279667..46283456-chr21:46286447..46289465,4	K562	blood:
10	chr21:46286677..46288930-chr6:170126669..170128404,2	K562	blood:
11	chr21:46222162..46224765-chr21:46287052..46289071,2	K562	blood:
12	chr21:46237355..46239033-chr21:46286989..46289637,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGB2-1	chr21:46286389-46288992	ENSG00000250713

No data

Variant related genes	Relation type
PTTG1IP	TF binding region
ENSG00000236519	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000184900	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2838714	0.86[AFR][1000 genomes]
rs28637887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8127305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8129155	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv913968	chr21:46249752-46301008	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1060233	chr21:46254075-46323401	Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription 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	32 gene(s)	inside rSNPs	diseases
11	nsv913969	chr21:46279505-46472929	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv544479	chr21:46280467-46323401	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv470907	chr21:46283669-46306161	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription 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	18 gene(s)	inside rSNPs	diseases
14	nsv459299	chr21:46283669-46311264	Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	nsv459300	chr21:46283669-46311264	Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	nsv587814	chr21:46283669-46311264	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46275600-46290600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:46278400-46289600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr21:46279600-46288800	Weak transcription	Fetal Kidney	kidney
4	chr21:46283400-46288800	Strong transcription	NHEK	skin
5	chr21:46284000-46289000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr21:46284800-46288600	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr21:46285000-46291600	Enhancers	Primary hematopoietic stem cells	blood
8	chr21:46285000-46291800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr21:46285200-46288600	Genic enhancers	Right Ventricle	heart
10	chr21:46285200-46288800	Genic enhancers	Osteobl	bone
11	chr21:46285200-46289000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr21:46285200-46289200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr21:46285200-46290000	Genic enhancers	Fetal Thymus	thymus
14	chr21:46285200-46290800	Enhancers	Right Atrium	heart
15	chr21:46285200-46291600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr21:46285400-46288600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr21:46285400-46289000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:46285400-46291600	Enhancers	Left Ventricle	heart
19	chr21:46285600-46288600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr21:46285600-46289400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr21:46285600-46291600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr21:46285600-46291800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr21:46285600-46292200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr21:46285800-46289000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr21:46285800-46289200	Enhancers	Brain Angular Gyrus	brain
26	chr21:46285800-46289400	Enhancers	Brain Substantia Nigra	brain
27	chr21:46285800-46290000	Enhancers	Brain Anterior Caudate	brain
28	chr21:46286000-46289000	Genic enhancers	K562	blood
29	chr21:46286000-46289600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr21:46286000-46289600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr21:46286000-46289600	Enhancers	Colon Smooth Muscle	Colon
32	chr21:46286000-46290600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr21:46286000-46290800	Enhancers	Brain Hippocampus Middle	brain
34	chr21:46286000-46291200	Enhancers	Stomach Mucosa	stomach
35	chr21:46286000-46291600	Enhancers	Liver	Liver
36	chr21:46286200-46290600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr21:46286600-46288600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr21:46286600-46288800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr21:46286600-46289000	Transcr. at gene 5' and 3'	HepG2	liver
40	chr21:46286600-46290400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr21:46286800-46289200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr21:46286800-46289600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr21:46286800-46289800	Enhancers	Aorta	Aorta
44	chr21:46286800-46290000	Enhancers	Psoas Muscle	Psoas
45	chr21:46287000-46289000	Enhancers	Brain Cingulate Gyrus	brain
46	chr21:46287000-46289600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr21:46287000-46290600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr21:46287200-46288800	Genic enhancers	HSMMtube	muscle
49	chr21:46287200-46289000	Strong transcription	Fetal Stomach	stomach
50	chr21:46287200-46289400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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