Variant report

Variant	rs3749180
Chromosome Location	chr3:20113989-20113990
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:20113304..20115252-chr3:20116309..20118672,2	K562	blood:
2	chr3:20111734..20113270-chr3:20113749..20115921,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13096186	0.88[EUR][1000 genomes]
rs13323791	0.86[ASN][1000 genomes]
rs13323914	0.86[ASN][1000 genomes]
rs17006525	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2140084	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2293142	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2365367	0.81[JPT][hapmap];0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2365368	0.85[AMR][1000 genomes]
rs2365369	0.84[AMR][1000 genomes]
rs2623079	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2686320	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686321	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2929389	0.89[EUR][1000 genomes]
rs2929390	0.88[EUR][1000 genomes]
rs2929391	0.88[EUR][1000 genomes]
rs2929392	0.88[EUR][1000 genomes]
rs2929394	0.96[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2948094	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2948095	0.82[EUR][1000 genomes]
rs2948096	0.86[EUR][1000 genomes]
rs3021408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828349	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858753	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858754	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858756	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4858757	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858758	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783606	0.86[ASN][1000 genomes]
rs6787947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71316245	0.93[EUR][1000 genomes]
rs73179773	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7637456	0.80[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7638345	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7640544	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9310605	0.86[ASN][1000 genomes]
rs9310608	0.87[ASN][1000 genomes]
rs9828532	0.87[ASN][1000 genomes]
rs9851449	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9917784	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
7	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
8	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
9	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
10	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
11	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3749180	UBE2E2	cis	parietal	SCAN
rs3749180	KAT2B	cis	parietal	SCAN
rs3749180	KAT2B	cis	Nerve Tibial	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20099000-20122600	Weak transcription	Aorta	Aorta
2	chr3:20099400-20122600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:20099400-20122800	Weak transcription	Lung	lung
4	chr3:20102800-20136800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:20103200-20114000	Weak transcription	Liver	Liver
6	chr3:20103200-20119400	Weak transcription	Fetal Intestine Small	intestine
7	chr3:20103200-20122200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:20106400-20122600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:20106800-20130800	Weak transcription	Fetal Intestine Large	intestine
10	chr3:20107000-20116800	Weak transcription	Small Intestine	intestine
11	chr3:20107000-20117000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:20107000-20122600	Weak transcription	Gastric	stomach
13	chr3:20107000-20122600	Weak transcription	Pancreas	Pancrea
14	chr3:20107000-20122600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:20107200-20122400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:20107800-20122600	Weak transcription	Spleen	Spleen
17	chr3:20107800-20122800	Weak transcription	Esophagus	oesophagus
18	chr3:20108200-20127600	Weak transcription	Ovary	ovary
19	chr3:20109000-20115200	Weak transcription	Hela-S3	cervix
20	chr3:20109000-20121200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:20109200-20115200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:20109200-20115200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:20109200-20122400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:20109600-20116800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:20110000-20124800	Weak transcription	Placenta	Placenta
26	chr3:20110200-20122400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:20110600-20115800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:20110600-20117800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:20110800-20114000	Weak transcription	HMEC	breast
30	chr3:20110800-20114200	Weak transcription	K562	blood
31	chr3:20110800-20121200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:20110800-20121200	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:20110800-20122000	Weak transcription	Stomach Mucosa	stomach
34	chr3:20111000-20115800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:20111000-20116200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:20111000-20122600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:20111400-20115000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:20111400-20115000	Enhancers	Psoas Muscle	Psoas
39	chr3:20111600-20114000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:20111600-20121600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:20112200-20115000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr3:20112200-20116400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:20112600-20116400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr3:20112600-20117000	Strong transcription	Primary T cells from cord blood	blood
45	chr3:20112600-20117600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:20112800-20114200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:20112800-20117200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr3:20112800-20117200	Enhancers	Brain Cingulate Gyrus	brain
49	chr3:20112800-20117800	Enhancers	Brain Angular Gyrus	brain
50	chr3:20113000-20114000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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