Variant report

Variant	rs4459901
Chromosome Location	chr3:133465699-133465700
allele	C/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	EP300	chr3:133464753-133465951	HepG2	liver:	n/a	chr3:133464957-133464973 chr3:133465936-133465949
2	SREBP1	chr3:133464736-133465929	HepG2	liver:	n/a	n/a
3	NFIC	chr3:133464671-133465951	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:133464703-133467781	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:133464533-133466088	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:133464701-133466024	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:133464731-133467233	HepG2	liver:	n/a	n/a
8	HEY1	chr3:133464668-133467472	HepG2	liver:	n/a	chr3:133465389-133465404
9	MYBL2	chr3:133464479-133466127	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:133464697-133466502	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:133464423-133479250	HepG2	liver:	n/a	n/a
12	MXI1	chr3:133464497-133466063	HepG2	liver:	n/a	n/a
13	CEBPD	chr3:133464897-133465890	HepG2	liver:	n/a	n/a
14	HEY1	chr3:133464270-133467811	HepG2	liver:	n/a	chr3:133465389-133465404
15	POLR2A	chr3:133464411-133467827	HepG2	liver:	n/a	n/a
16	MBD4	chr3:133464603-133466405	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TF	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10433417	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10935073	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935074	0.84[EUR][1000 genomes]
rs11921527	0.92[EUR][1000 genomes]
rs12493887	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12639304	0.92[EUR][1000 genomes]
rs12769	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4075352	0.85[ASN][1000 genomes]
rs4355280	0.81[ASN][1000 genomes]
rs4481157	0.87[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4525863	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6439431	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6439435	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6774822	0.92[EUR][1000 genomes]
rs6775042	0.92[EUR][1000 genomes]
rs6777860	0.96[EUR][1000 genomes]
rs6780650	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6782523	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6787177	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6797713	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6798547	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7646118	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8177177	0.91[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs8177178	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8177197	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8177204	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8177224	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9829019	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9830001	0.86[CEU][hapmap]
rs9831392	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9869257	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9869535	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers 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	9 gene(s)	inside rSNPs	diseases
4	nsv877507	chr3:133465201-133473516	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133464400-133465800	Enhancers	Pancreas	Pancrea
2	chr3:133464400-133466400	Weak transcription	K562	blood
3	chr3:133464600-133465800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:133464800-133466000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
5	chr3:133464800-133467000	Active TSS	Brain Anterior Caudate	brain
6	chr3:133464800-133467000	Active TSS	Brain Substantia Nigra	brain
7	chr3:133464800-133467000	Bivalent/Poised TSS	HepG2	liver
8	chr3:133464800-133467200	Active TSS	Brain Hippocampus Middle	brain
9	chr3:133464800-133468200	Active TSS	Brain Cingulate Gyrus	brain
10	chr3:133464800-133468400	Active TSS	Brain Angular Gyrus	brain
11	chr3:133465000-133466000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:133465000-133468200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:133465000-133468400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr3:133465400-133465800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:133465400-133465800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr3:133465400-133466200	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr3:133465400-133468400	Weak transcription	Esophagus	oesophagus
18	chr3:133465600-133465800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:133465600-133465800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:133465600-133465800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:133465600-133465800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:133465600-133465800	Bivalent Enhancer	Right Ventricle	heart
23	chr3:133465600-133466000	Active TSS	Liver	Liver
24	chr3:133465600-133466200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:133465600-133466600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:133465600-133483000	Weak transcription	Brain Germinal Matrix	brain

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