Variant report

Variant	rs3811781
Chromosome Location	chr4:53729166-53729167
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	POLR2A	chr4:53728148-53729427	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF7	chr4:53728148-53729570	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3A	chr4:53726721-53729851	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:53728021-53729235	K562	blood:	n/a	n/a
5	TBP	chr4:53728185-53729291	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr4:53726951-53732052	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr4:53727789-53729591	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr4:53727777-53729216	K562	blood:	n/a	chr4:53728200-53728210 chr4:53728643-53728654 chr4:53728435-53728444 chr4:53728439-53728449
9	POLR2A	chr4:53729158-53729216	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:53728015-53729261	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTBP2	chr4:53727338-53729596	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr4:53727407-53729218	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:53525430..53527688-chr4:53726700..53729187,4	MCF-7	breast:
2	chr4:53586938..53589965-chr4:53727574..53731676,3	MCF-7	breast:
3	chr4:53577401..53580169-chr4:53726393..53730142,5	MCF-7	breast:

Variant related genes	Relation type
RASL11B	TF binding region
ENSG00000248866	Chromatin interaction
ENSG00000226950	Chromatin interaction
ENSG00000264585	Chromatin interaction
ENSG00000109189	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000248375	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10517269	0.89[AMR][1000 genomes]
rs11938159	0.87[AMR][1000 genomes]
rs11939448	0.85[AMR][1000 genomes]
rs17082074	0.84[ASN][1000 genomes]
rs17082087	0.80[AMR][1000 genomes]
rs17082091	0.85[AMR][1000 genomes]
rs2200225	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41279517	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211634	0.80[AFR][1000 genomes]
rs58461944	0.80[AMR][1000 genomes]
rs58577680	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59042894	0.85[AMR][1000 genomes]
rs6554054	0.87[AMR][1000 genomes]
rs6554057	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817433	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6818178	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6833350	0.80[EUR][1000 genomes]
rs6838718	0.87[AMR][1000 genomes]
rs6848200	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855240	0.80[EUR][1000 genomes]
rs73814868	0.89[AMR][1000 genomes]
rs73814875	0.95[ASN][1000 genomes]
rs73814883	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814886	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73814893	0.80[AFR][1000 genomes]
rs73814894	0.80[AFR][1000 genomes]
rs7655781	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7663419	0.85[AMR][1000 genomes]
rs7670068	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7685816	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7688141	0.87[AMR][1000 genomes]
rs7693568	0.85[AMR][1000 genomes]
rs7699960	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs881744	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3360858	chr4:53727420-53729968	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53727400-53729600	Active TSS	Brain Angular Gyrus	brain
2	chr4:53727400-53729600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:53727600-53729200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr4:53727600-53729200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
5	chr4:53727600-53729200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr4:53727600-53729600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:53727600-53729600	Active TSS	NHDF-Ad	bronchial
8	chr4:53727800-53729200	Flanking Active TSS	HMEC	breast
9	chr4:53727800-53729400	Flanking Active TSS	Pancreas	Pancrea
10	chr4:53727800-53730800	Active TSS	Aorta	Aorta
11	chr4:53727800-53731800	Active TSS	Fetal Kidney	kidney
12	chr4:53728000-53729200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr4:53728000-53729200	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr4:53728000-53729200	Active TSS	HSMM	muscle
15	chr4:53728000-53729200	Active TSS	HSMMtube	muscle
16	chr4:53728000-53729400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:53728000-53729400	Active TSS	Brain Cingulate Gyrus	brain
18	chr4:53728000-53729400	Active TSS	Ovary	ovary
19	chr4:53728000-53729600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:53728000-53729600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr4:53728000-53729800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:53728000-53730000	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr4:53728000-53730000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:53728000-53730200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:53728000-53730400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:53728200-53729400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:53728200-53729400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr4:53728200-53729400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:53728200-53729400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:53728200-53729600	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr4:53728200-53729600	Active TSS	Fetal Brain Female	brain
32	chr4:53728200-53729800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:53728200-53729800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:53728200-53729800	Active TSS	Fetal Heart	heart
35	chr4:53728400-53729200	Active TSS	H1 Cell Line	embryonic stem cell
36	chr4:53728600-53729200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:53728600-53729200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr4:53728600-53729200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
39	chr4:53728600-53729200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
40	chr4:53728600-53729200	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr4:53728600-53729200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
42	chr4:53728600-53729200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
43	chr4:53728600-53729200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
44	chr4:53728600-53729200	Flanking Active TSS	Esophagus	oesophagus
45	chr4:53728600-53729200	Flanking Active TSS	Gastric	stomach
46	chr4:53728600-53729200	Flanking Active TSS	Lung	lung
47	chr4:53728600-53729200	Flanking Active TSS	Right Ventricle	heart
48	chr4:53728600-53729200	Flanking Bivalent TSS/Enh	Thymus	Thymus
49	chr4:53728600-53729200	Flanking Active TSS	NH-A	brain
50	chr4:53728600-53729400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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