Variant report

Variant	rs4652461
Chromosome Location	chr1:180010702-180010703
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	SPI1	chr1:180010471-180011170	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
CEP350	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10798729	0.93[JPT][hapmap]
rs10913916	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs10913927	0.80[JPT][hapmap]
rs12075450	0.84[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap]
rs12091685	0.95[GIH][hapmap];0.81[EUR][1000 genomes]
rs16855164	1.00[ASN][1000 genomes]
rs1981314	0.94[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2319676	0.94[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2319677	0.84[CEU][hapmap]
rs2319773	0.88[ASN][1000 genomes]
rs2477106	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2477107	0.90[ASN][1000 genomes]
rs2477109	0.88[ASN][1000 genomes]
rs2477113	0.86[ASN][1000 genomes]
rs2477115	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2477117	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2477119	0.84[ASN][1000 genomes]
rs2483622	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[YRI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2501608	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501614	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501618	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2501619	0.85[ASN][1000 genomes]
rs2501621	0.81[CHB][hapmap];0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs3123521	0.91[ASN][1000 genomes]
rs3767201	0.94[CHD][hapmap];0.87[JPT][hapmap]
rs3818999	0.87[JPT][hapmap]
rs3930305	0.80[JPT][hapmap]
rs4147170	0.84[CEU][hapmap]
rs4256775	0.80[JPT][hapmap]
rs4263962	0.81[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs4379644	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4622030	0.84[CEU][hapmap]
rs4651055	0.94[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs4652464	0.88[ASN][1000 genomes]
rs4652465	0.80[JPT][hapmap]
rs551607	0.80[ASW][hapmap]
rs55953436	0.87[EUR][1000 genomes]
rs55971224	0.86[EUR][1000 genomes]
rs6425602	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425603	0.80[JPT][hapmap]
rs6425606	0.90[ASW][hapmap];0.84[CEU][hapmap]
rs6425607	0.84[CEU][hapmap]
rs6657347	0.80[JPT][hapmap]
rs6659911	0.96[ASN][1000 genomes]
rs6660984	0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6676989	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6682558	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs6692394	0.81[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs7521948	1.00[ASW][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7547954	0.81[EUR][1000 genomes]
rs9286932	0.80[JPT][hapmap]
rs9425852	0.97[ASN][1000 genomes]
rs9425853	0.84[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425854	0.93[JPT][hapmap]
rs9425857	0.92[ASN][1000 genomes]
rs9425858	0.89[ASN][1000 genomes]
rs9425859	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9425861	0.80[JPT][hapmap]
rs9887843	0.95[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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv3755	chr1:179998860-180043554	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv1000698	chr1:179999669-180042521	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
2	chr1:179964000-180014200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:179965800-180013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:179973000-180010800	Weak transcription	Psoas Muscle	Psoas
6	chr1:179976200-180063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:179980400-180027400	Strong transcription	Dnd41	blood
8	chr1:179981000-180027200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr1:179981000-180059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:179981600-180012000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:179985600-180024800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:179989800-180034200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:179990000-180012000	Weak transcription	Gastric	stomach
15	chr1:179990000-180012200	Weak transcription	Stomach Mucosa	stomach
16	chr1:179990000-180025600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:179990200-180025400	Weak transcription	Pancreas	Pancrea
18	chr1:179992400-180012000	Weak transcription	Right Ventricle	heart
19	chr1:179992400-180031400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:179992400-180032200	Weak transcription	Esophagus	oesophagus
21	chr1:179992600-180010800	Weak transcription	Colonic Mucosa	Colon
22	chr1:179993800-180010800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:179998000-180010800	Weak transcription	HSMMtube	muscle
24	chr1:180000200-180029200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:180000400-180016600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:180000600-180026600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:180000600-180039800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:180000800-180083400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:180001400-180010800	Weak transcription	HepG2	liver
30	chr1:180001400-180011000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:180002400-180027000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:180002400-180085000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:180002800-180015400	Strong transcription	Fetal Lung	lung
34	chr1:180002800-180027200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:180003800-180012000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:180004000-180010800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:180004000-180010800	Weak transcription	Brain Substantia Nigra	brain
38	chr1:180004000-180011400	Weak transcription	Brain Anterior Caudate	brain
39	chr1:180004200-180011800	Weak transcription	Fetal Kidney	kidney
40	chr1:180004200-180025600	Weak transcription	Lung	lung
41	chr1:180004400-180010800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:180004400-180011000	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:180004600-180011000	Weak transcription	Fetal Heart	heart
44	chr1:180005400-180010800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:180005800-180022800	Weak transcription	Small Intestine	intestine
46	chr1:180006200-180010800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:180006200-180010800	Weak transcription	Aorta	Aorta
48	chr1:180006200-180010800	Weak transcription	Fetal Brain Female	brain
49	chr1:180006400-180010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:180006600-180011200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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