Variant report

Variant	rs7642664
Chromosome Location	chr3:110788941-110788942
allele	A/G
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	chr3:110788902-110792346	IMR90	lung:	n/a	n/a
2	POLR2A	chr3:110788638-110791793	H1-neurons	neurons:	n/a	n/a
3	REST	chr3:110788492-110789361	H1-neurons	neurons:	n/a	n/a
4	CHD1	chr3:110788894-110792602	IMR90	lung:	n/a	chr3:110790569-110790579 chr3:110791180-110791190
5	SIN3A	chr3:110788772-110791820	H1-hESC	embryonic stem cell:	n/a	chr3:110789838-110789851
6	POLR2A	chr3:110788655-110789382	H1-neurons	neurons:	n/a	n/a
7	CEBPB	chr3:110788794-110789262	H1-hESC	embryonic stem cell:	n/a	n/a
8	CEBPB	chr3:110788704-110789073	IMR90	lung:	n/a	n/a
9	RAD21	chr3:110788763-110792538	IMR90	lung:	n/a	n/a
10	POLR2A	chr3:110788827-110789253	HCT-116	colon:	n/a	n/a
11	RAD21	chr3:110788919-110790379	SK-N-SH_RA	brain:	n/a	n/a
12	MXI1	chr3:110788792-110792832	IMR90	lung:	n/a	n/a
13	MAFF	chr3:110788887-110789031	HepG2	liver:	n/a	n/a
14	CEBPB	chr3:110788755-110789058	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:110788707-110791269	ProgFib	skin:	n/a	n/a
16	MAZ	chr3:110788798-110791528	IMR90	lung:	n/a	chr3:110789520-110789530

Variant related genes	Relation type
PVRL3	TF binding region
PVRL3-AS1	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12185974	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1370	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1801650	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1824709	1.00[EUR][1000 genomes]
rs4634159	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs55987847	0.88[AFR][1000 genomes]
rs56324569	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56724510	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58112872	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61190717	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61219682	0.81[AFR][1000 genomes]
rs6437943	0.93[EUR][1000 genomes]
rs73852350	0.88[AFR][1000 genomes]
rs73852352	0.88[AFR][1000 genomes]
rs73852384	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73852394	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73852397	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73852398	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73852399	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73852401	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73852402	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854903	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854905	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854910	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73854911	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854912	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854913	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854914	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854915	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854916	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854919	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854920	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73854921	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854922	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854923	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73854926	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854927	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854928	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73854929	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7615927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7616280	1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7622397	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9844779	0.93[EUR][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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110777800-110789000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:110784600-110789000	Weak transcription	Left Ventricle	heart
3	chr3:110787000-110789000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:110788000-110789000	Active TSS	Fetal Brain Female	brain
5	chr3:110788200-110789200	Active TSS	Fetal Brain Male	brain
6	chr3:110788200-110789400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:110788400-110789000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:110788400-110789000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:110788400-110791600	Active TSS	Brain Hippocampus Middle	brain
10	chr3:110788400-110792200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:110788400-110792400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr3:110788400-110793000	Active TSS	Brain Angular Gyrus	brain
13	chr3:110788600-110789000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr3:110788600-110789000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:110788600-110789000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:110788600-110789000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:110788600-110789000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr3:110788600-110789000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:110788600-110789000	Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr3:110788600-110789000	Enhancers	Adipose Nuclei	Adipose
21	chr3:110788600-110789000	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr3:110788600-110789000	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:110788600-110789200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:110788600-110789200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:110788600-110789200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:110788600-110789200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr3:110788600-110789200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
28	chr3:110788600-110789200	Flanking Active TSS	NHLF	lung
29	chr3:110788600-110789400	Flanking Active TSS	Fetal Intestine Small	intestine
30	chr3:110788600-110789600	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr3:110788600-110791600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:110788600-110791600	Active TSS	Brain Cingulate Gyrus	brain
33	chr3:110788600-110792000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr3:110788600-110792000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:110788600-110792400	Active TSS	Fetal Lung	lung
36	chr3:110788600-110794200	Active TSS	Ovary	ovary
37	chr3:110788600-110794600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr3:110788800-110789000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
39	chr3:110788800-110789000	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:110788800-110789000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr3:110788800-110789000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:110788800-110789000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:110788800-110789000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:110788800-110789000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:110788800-110789000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:110788800-110789000	Enhancers	Liver	Liver
47	chr3:110788800-110789000	Active TSS	Brain Germinal Matrix	brain
48	chr3:110788800-110789000	Enhancers	Colon Smooth Muscle	Colon
49	chr3:110788800-110789000	Active TSS	Fetal Muscle Trunk	muscle
50	chr3:110788800-110789000	Flanking Active TSS	Placenta	Placenta

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