Variant report

Variant	rs5753551
Chromosome Location	chr22:31691743-31691744
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	RFX5	chr22:31691473-31692187	Hela-S3	cervix:	n/a	n/a
2	GATA3	chr22:31691686-31692364	SK-N-SH	brain:	n/a	n/a
3	GATA2	chr22:31691660-31692528	HUVEC	blood vessel:	n/a	n/a
4	ARID3A	chr22:31691726-31692293	K562	blood:	n/a	n/a
5	FOS	chr22:31691622-31692628	MCF10A-Er-Src	breast:	n/a	chr22:31692541-31692550 chr22:31692017-31692028
6	CUX1	chr22:31691549-31692326	K562	blood:	n/a	n/a
7	TEAD4	chr22:31691725-31692152	K562	blood:	n/a	n/a
8	GATA1	chr22:31691721-31692363	PBDE	blood:	n/a	n/a
9	IRF1	chr22:31691726-31692267	K562	blood:	n/a	n/a
10	BRCA1	chr22:31691681-31691915	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr22:31691697-31691793	MCF10A-Er-Src	breast:	n/a	n/a
12	JUN	chr22:31691642-31692202	K562	blood:	n/a	n/a
13	FOS	chr22:31691729-31692892	MCF10A-Er-Src	breast:	n/a	chr22:31692541-31692550 chr22:31692017-31692028

No.	Distal block	Cell Line	Cell type
1	chr22:31689960..31693778-chr22:31698735..31700616,3	MCF-7	breast:
2	chr22:31683915..31694680-chr22:31733392..31744713,34	MCF-7	breast:
3	chr22:31689966..31691795-chr22:31696089..31697952,2	K562	blood:

Variant related genes	Relation type
PIK3IP1	TF binding region
ENSG00000213888	Chromatin interaction
ENSG00000100105	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1005624	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1034587	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10428007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11089491	0.85[ASN][1000 genomes]
rs12106582	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12627805	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12627941	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12628752	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17220369	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2027982	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2072193	0.80[JPT][hapmap]
rs2073858	0.86[ASN][1000 genomes]
rs2074735	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2239905	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239906	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267169	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2267170	0.89[ASN][1000 genomes]
rs2267171	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283878	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283880	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2413041	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28514306	0.87[ASN][1000 genomes]
rs28709894	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34184692	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3761431	0.81[CHB][hapmap]
rs3788428	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs4561750	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4645077	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4820040	0.89[EUR][1000 genomes]
rs4820949	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4820952	0.83[ASN][1000 genomes]
rs4820964	0.93[ASN][1000 genomes]
rs4820965	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55737363	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55900008	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5749222	0.82[YRI][hapmap]
rs5749226	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5749231	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs5749232	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749237	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs5749260	0.81[ASN][1000 genomes]
rs5753488	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753499	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753518	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs5753528	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753531	0.89[ASN][1000 genomes]
rs5753550	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753559	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs5753560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753573	0.94[EUR][1000 genomes]
rs5753577	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58315696	0.89[ASN][1000 genomes]
rs5997898	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs5997940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs61006749	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62236175	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62237396	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62237398	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62237399	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62237400	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62237404	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62237436	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68136222	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72617294	0.86[ASN][1000 genomes]
rs72617295	0.90[ASN][1000 genomes]
rs73158522	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs737809	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs886074	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9609263	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31688400-31693400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:31688600-31691800	Weak transcription	Left Ventricle	heart
3	chr22:31688800-31692000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr22:31688800-31692000	Weak transcription	Colonic Mucosa	Colon
5	chr22:31688800-31692400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:31688800-31692400	Weak transcription	Fetal Lung	lung
7	chr22:31688800-31693000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr22:31689000-31691800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:31689000-31696400	Weak transcription	HepG2	liver
10	chr22:31689200-31692600	Enhancers	Primary B cells from cord blood	blood
11	chr22:31689200-31693000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr22:31689200-31696400	Weak transcription	Liver	Liver
13	chr22:31689200-31696400	Weak transcription	Right Atrium	heart
14	chr22:31689400-31709000	Weak transcription	Placenta	Placenta
15	chr22:31689600-31692000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr22:31689800-31695600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr22:31690000-31691800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr22:31690000-31691800	Weak transcription	Colon Smooth Muscle	Colon
19	chr22:31690200-31704200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr22:31690400-31692000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr22:31691200-31692200	Enhancers	Small Intestine	intestine
22	chr22:31691200-31692400	Enhancers	K562	blood
23	chr22:31691200-31692800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr22:31691200-31693000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr22:31691200-31693000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr22:31691200-31693000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr22:31691200-31693200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr22:31691200-31693200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr22:31691200-31693200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr22:31691200-31693400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr22:31691200-31693400	Enhancers	Rectal Smooth Muscle	rectum
32	chr22:31691400-31691800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr22:31691400-31691800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr22:31691400-31692000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr22:31691400-31692200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr22:31691400-31692200	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr22:31691400-31692200	Enhancers	NHDF-Ad	bronchial
38	chr22:31691400-31692400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr22:31691400-31692400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr22:31691400-31692600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr22:31691400-31692600	Enhancers	Stomach Mucosa	stomach
42	chr22:31691400-31692800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr22:31691400-31692800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:31691400-31692800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr22:31691400-31692800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr22:31691400-31692800	Enhancers	NHLF	lung
47	chr22:31691400-31693000	Active TSS	Primary T cells fromperipheralblood	blood
48	chr22:31691400-31693000	Enhancers	Brain Angular Gyrus	brain
49	chr22:31691400-31693000	Enhancers	HSMM	muscle
50	chr22:31691400-31693000	Enhancers	HUVEC	blood vessel

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