Variant report

Variant	rs3788076
Chromosome Location	chr21:45323412-45323413
allele	G/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	MXI1	chr21:45323169-45324167	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr21:45323281-45323688	K562	blood:	n/a	n/a
3	ELF1	chr21:45323301-45323535	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:45285418..45288376-chr21:45321880..45324021,2	K562	blood:
2	chr21:45322017..45325690-chr21:45333512..45336768,4	MCF-7	breast:
3	chr21:45138873..45140512-chr21:45322056..45323617,2	K562	blood:

Variant related genes	Relation type
AGPAT3	TF binding region
ENSG00000160216	Chromatin interaction
ENSG00000160209	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2070545	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2329629	1.00[JPT][hapmap]
rs2838417	1.00[CHB][hapmap]
rs2838418	1.00[CHB][hapmap]
rs2838442	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2838443	1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs3737358	0.82[JPT][hapmap]
rs3788083	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs3788089	1.00[JPT][hapmap]
rs3819608	1.00[CHB][hapmap]
rs7278317	1.00[JPT][hapmap]
rs73371168	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8134181	1.00[YRI][hapmap];0.82[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	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
2	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	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
4	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1066284	chr21:45249549-45343314	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45287400-45330200	Weak transcription	Fetal Kidney	kidney
2	chr21:45288200-45324200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr21:45301000-45328400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr21:45301400-45326000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr21:45305000-45328000	Weak transcription	NHEK	skin
6	chr21:45305000-45332600	Weak transcription	Colon Smooth Muscle	Colon
7	chr21:45305200-45323600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:45305200-45327600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr21:45309800-45330600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr21:45314000-45330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr21:45314200-45323600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr21:45314400-45332000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr21:45314800-45324400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr21:45314800-45329600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr21:45314800-45336000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr21:45316600-45324600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr21:45316600-45336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr21:45319200-45324600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr21:45319200-45328400	Weak transcription	A549	lung
20	chr21:45319400-45324600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr21:45319400-45328800	Weak transcription	HepG2	liver
22	chr21:45319600-45325600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr21:45319600-45331200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr21:45319800-45323800	Weak transcription	Aorta	Aorta
25	chr21:45319800-45324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr21:45319800-45331000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr21:45319800-45331800	Weak transcription	Brain Germinal Matrix	brain
28	chr21:45320000-45325600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr21:45320000-45332400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr21:45320200-45323800	Weak transcription	Dnd41	blood
31	chr21:45320400-45323800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr21:45320600-45323800	Weak transcription	Thymus	Thymus
33	chr21:45320800-45323600	Weak transcription	Fetal Brain Female	brain
34	chr21:45320800-45325600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr21:45321000-45323600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr21:45321000-45324200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr21:45321000-45324200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr21:45321000-45325200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr21:45321000-45325800	Weak transcription	Primary B cells from cord blood	blood
40	chr21:45321000-45327800	Weak transcription	Brain Anterior Caudate	brain
41	chr21:45321000-45331400	Weak transcription	Brain Substantia Nigra	brain
42	chr21:45321200-45323600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr21:45321200-45323600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr21:45321600-45324400	Enhancers	Liver	Liver
45	chr21:45322000-45323800	Enhancers	HUVEC	blood vessel
46	chr21:45322200-45324000	Enhancers	Fetal Lung	lung
47	chr21:45322200-45324000	Enhancers	NHLF	lung
48	chr21:45322400-45323800	Enhancers	Fetal Muscle Leg	muscle
49	chr21:45322400-45323800	Enhancers	Ovary	ovary
50	chr21:45322400-45324000	Enhancers	Gastric	stomach

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