Variant report

Variant	rs2929402
Chromosome Location	chr3:20096110-20096111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20094893..20096727-chr3:20227964..20230863,2	MCF-7	breast:
2	chr3:20087468..20090751-chr3:20095333..20097422,3	MCF-7	breast:
3	chr3:19987759..19990074-chr3:20094320..20096186,3	MCF-7	breast:
4	chr3:19919756..19921311-chr3:20094992..20097825,2	K562	blood:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2929401	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2948082	0.96[ASN][1000 genomes]
rs7620608	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7628266	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
7	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS 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	9 gene(s)	inside rSNPs	diseases
9	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2929402	KAT2B	cis	cerebellum	SCAN
rs2929402	KAT2B	cis	brain	BrainEAC

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20083000-20098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:20085200-20098200	Weak transcription	Fetal Kidney	kidney
3	chr3:20086200-20096800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:20086200-20102800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:20087600-20099400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:20089800-20096200	Weak transcription	Brain Germinal Matrix	brain
7	chr3:20090200-20096400	Weak transcription	Fetal Brain Male	brain
8	chr3:20090200-20096400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:20090200-20098400	Weak transcription	Ovary	ovary
10	chr3:20090400-20096400	Weak transcription	Fetal Stomach	stomach
11	chr3:20090800-20099200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:20090800-20100600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:20092200-20096200	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:20093000-20096400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:20094000-20097600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:20094200-20099400	Enhancers	Fetal Thymus	thymus
17	chr3:20095200-20098400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:20095400-20096200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:20095400-20096400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr3:20095400-20096400	Enhancers	Brain Anterior Caudate	brain
21	chr3:20095400-20099600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:20095600-20096200	Enhancers	Thymus	Thymus
23	chr3:20095600-20097200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:20095600-20097200	Enhancers	Left Ventricle	heart
25	chr3:20095600-20097200	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr3:20095600-20097600	Enhancers	Primary B cells from cord blood	blood
27	chr3:20095600-20099000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:20095600-20099400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr3:20095600-20099600	Enhancers	Liver	Liver
30	chr3:20095600-20099800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:20095600-20100000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:20095600-20100200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:20095600-20100200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:20095600-20100400	Enhancers	Fetal Heart	heart
35	chr3:20095600-20100800	Enhancers	Placenta	Placenta
36	chr3:20095800-20096200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr3:20095800-20096400	Enhancers	Brain Substantia Nigra	brain
38	chr3:20095800-20096400	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr3:20095800-20096400	Enhancers	Hela-S3	cervix
40	chr3:20095800-20096600	Enhancers	Osteobl	bone
41	chr3:20095800-20096800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:20095800-20096800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:20095800-20096800	Enhancers	Brain Hippocampus Middle	brain
44	chr3:20095800-20097000	Enhancers	NHDF-Ad	bronchial
45	chr3:20095800-20097000	Enhancers	NHLF	lung
46	chr3:20095800-20097200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:20095800-20097200	Enhancers	HSMM	muscle
48	chr3:20095800-20097400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:20095800-20097400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:20095800-20097400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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