Variant report

Variant	rs873133
Chromosome Location	chr3:110789199-110789200
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	MAX	chr3:110788996-110789722	H1-hESC	embryonic stem cell:	n/a	chr3:110789520-110789530
5	CHD1	chr3:110788894-110792602	IMR90	lung:	n/a	chr3:110790569-110790579 chr3:110791180-110791190
6	MXI1	chr3:110789050-110791341	HepG2	liver:	n/a	n/a
7	SIN3A	chr3:110788772-110791820	H1-hESC	embryonic stem cell:	n/a	chr3:110789838-110789851
8	JUND	chr3:110789104-110791395	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr3:110789085-110790377	U87	brain:	n/a	n/a
10	GATA2	chr3:110788986-110790755	SH-SY5Y	brain:	n/a	n/a
11	CTCF	chr3:110789145-110789227	Kidney_OC	kidney:	n/a	n/a
12	POLR2A	chr3:110789112-110789219	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:110789026-110790795	HCT-116	colon:	n/a	n/a
14	POLR2A	chr3:110788655-110789382	H1-neurons	neurons:	n/a	n/a
15	CEBPB	chr3:110788794-110789262	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr3:110788992-110789257	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr3:110788763-110792538	IMR90	lung:	n/a	n/a
18	POLR2A	chr3:110788827-110789253	HCT-116	colon:	n/a	n/a
19	RAD21	chr3:110788919-110790379	SK-N-SH_RA	brain:	n/a	n/a
20	MAX	chr3:110789085-110791581	HepG2	liver:	n/a	chr3:110789520-110789530
21	MAX	chr3:110789053-110789338	H1-hESC	embryonic stem cell:	n/a	n/a
22	MXI1	chr3:110788792-110792832	IMR90	lung:	n/a	n/a
23	POLR2A	chr3:110789082-110791825	HepG2	liver:	n/a	n/a
24	MXI1	chr3:110789146-110789825	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr3:110789147-110790961	HepG2	liver:	n/a	n/a
26	MAX	chr3:110789106-110791640	HepG2	liver:	n/a	chr3:110789520-110789530
27	POLR2A	chr3:110788707-110791269	ProgFib	skin:	n/a	n/a
28	MAZ	chr3:110788798-110791528	IMR90	lung:	n/a	chr3:110789520-110789530
29	POLR2A	chr3:110789135-110791066	Gliobla	brain:	n/a	n/a

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

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10511291	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1462299	0.82[EUR][1000 genomes]
rs1477846	0.87[ASN][1000 genomes]
rs1477848	0.87[ASN][1000 genomes]
rs16857350	0.82[EUR][1000 genomes]
rs16857536	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2126714	0.90[ASN][1000 genomes]
rs57043424	0.83[ASN][1000 genomes]
rs60037602	0.82[EUR][1000 genomes]
rs60585479	0.83[ASN][1000 genomes]
rs66624862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72934030	0.82[EUR][1000 genomes]
rs72934034	0.82[EUR][1000 genomes]
rs72934100	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72935934	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72935952	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935959	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935966	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935968	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72935989	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72935999	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72937905	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72937952	0.83[ASN][1000 genomes]
rs72937960	0.83[ASN][1000 genomes]
rs72937968	0.83[ASN][1000 genomes]
rs72937972	0.83[ASN][1000 genomes]
rs72948795	0.82[EUR][1000 genomes]
rs72948800	0.82[EUR][1000 genomes]
rs7433877	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648752	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs873132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9288918	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9288919	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9853370	0.91[EUR][1000 genomes];0.87[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	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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110788200-110789200	Active TSS	Fetal Brain Male	brain
2	chr3:110788200-110789400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:110788400-110791600	Active TSS	Brain Hippocampus Middle	brain
4	chr3:110788400-110792200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:110788400-110792400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:110788400-110793000	Active TSS	Brain Angular Gyrus	brain
7	chr3:110788600-110789200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:110788600-110789200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:110788600-110789200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:110788600-110789200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr3:110788600-110789200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
12	chr3:110788600-110789200	Flanking Active TSS	NHLF	lung
13	chr3:110788600-110789400	Flanking Active TSS	Fetal Intestine Small	intestine
14	chr3:110788600-110789600	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr3:110788600-110791600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:110788600-110791600	Active TSS	Brain Cingulate Gyrus	brain
17	chr3:110788600-110792000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr3:110788600-110792000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:110788600-110792400	Active TSS	Fetal Lung	lung
20	chr3:110788600-110794200	Active TSS	Ovary	ovary
21	chr3:110788600-110794600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr3:110788800-110789200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:110788800-110789200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:110788800-110789200	Enhancers	Aorta	Aorta
25	chr3:110788800-110789200	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr3:110788800-110789200	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr3:110788800-110789200	Enhancers	Stomach Mucosa	stomach
28	chr3:110788800-110789200	Flanking Active TSS	HepG2	liver
29	chr3:110788800-110789200	Flanking Active TSS	HSMM	muscle
30	chr3:110788800-110789400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:110788800-110789400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:110788800-110789400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:110788800-110789400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:110788800-110789400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr3:110788800-110789400	Flanking Active TSS	HSMMtube	muscle
36	chr3:110788800-110789400	Flanking Active TSS	NH-A	brain
37	chr3:110788800-110789600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr3:110788800-110789600	Flanking Active TSS	Fetal Heart	heart
39	chr3:110788800-110789600	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr3:110788800-110789600	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr3:110788800-110789600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr3:110788800-110789600	Flanking Active TSS	Osteobl	bone
43	chr3:110788800-110790600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:110788800-110791800	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr3:110788800-110792200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:110788800-110792400	Active TSS	H9 Cell Line	embryonic stem cell
47	chr3:110788800-110792600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:110788800-110792600	Active TSS	Rectal Smooth Muscle	rectum
49	chr3:110788800-110792600	Active TSS	Right Atrium	heart
50	chr3:110788800-110793200	Active TSS	Fetal Kidney	kidney

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