Variant report

Variant	rs5752903
Chromosome Location	chr22:29769306-29769307
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29764682..29767147-chr22:29767285..29770224,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100280	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11090564	0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs131180	0.82[ASN][1000 genomes]
rs140062	0.88[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs140063	0.82[ASN][1000 genomes]
rs140066	0.83[ASN][1000 genomes]
rs174759	0.85[ASN][1000 genomes]
rs174761	0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs174762	0.88[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap]
rs174764	0.88[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs174765	0.86[ASN][1000 genomes]
rs174766	0.88[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs174769	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs174770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174771	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174775	0.89[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2071578	0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.91[ASN][1000 genomes]
rs2072051	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267132	0.80[CHB][hapmap]
rs2267133	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs2267135	0.81[ASN][1000 genomes]
rs2267137	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2283849	0.88[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs2283850	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301290	0.88[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs2301585	0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2857462	0.81[ASN][1000 genomes]
rs28755	0.87[ASN][1000 genomes]
rs3788410	0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap]
rs3788411	0.88[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs4820803	0.88[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap]
rs4820804	0.88[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap]
rs5763138	0.88[CHB][hapmap];0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs5763139	0.88[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs5763172	0.81[ASN][1000 genomes]
rs5763178	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006090	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs6006098	0.88[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs6006115	0.81[ASN][1000 genomes]
rs715494	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs879580	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs9537	0.88[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs98069	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv914961	chr22:29755888-29817506	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv914962	chr22:29755888-29823768	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	esv2580719	chr22:29759273-29816494	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	esv3498689	chr22:29763576-29812598	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	esv3498690	chr22:29763576-29812598	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv3382633	chr22:29764347-29814462	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv459868	chr22:29767925-29807855	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv459869	chr22:29767925-29807855	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv588882	chr22:29767925-29807855	Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29741000-29782800	Weak transcription	Hela-S3	cervix
2	chr22:29753000-29777600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr22:29754600-29770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr22:29755000-29772200	Weak transcription	Aorta	Aorta
5	chr22:29755000-29783800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:29755200-29773800	Weak transcription	Stomach Mucosa	stomach
7	chr22:29755200-29781000	Weak transcription	Fetal Brain Male	brain
8	chr22:29755200-29782800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr22:29755400-29783600	Weak transcription	Fetal Kidney	kidney
10	chr22:29755600-29771400	Weak transcription	Psoas Muscle	Psoas
11	chr22:29755600-29778600	Weak transcription	Fetal Lung	lung
12	chr22:29755800-29776600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr22:29756000-29771400	Weak transcription	Esophagus	oesophagus
14	chr22:29756000-29771400	Weak transcription	HMEC	breast
15	chr22:29756000-29771800	Weak transcription	NHLF	lung
16	chr22:29756000-29772200	Weak transcription	Right Atrium	heart
17	chr22:29756000-29776200	Weak transcription	Small Intestine	intestine
18	chr22:29756000-29779800	Weak transcription	Brain Germinal Matrix	brain
19	chr22:29756000-29783600	Weak transcription	Right Ventricle	heart
20	chr22:29756000-29783800	Weak transcription	Ovary	ovary
21	chr22:29756200-29779200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr22:29756400-29770400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr22:29756400-29772200	Weak transcription	Fetal Heart	heart
24	chr22:29756400-29782600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr22:29758200-29771800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr22:29758200-29777000	Weak transcription	Colonic Mucosa	Colon
27	chr22:29762600-29771400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr22:29762800-29770800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:29762800-29771800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr22:29762800-29777200	Weak transcription	Fetal Brain Female	brain
31	chr22:29764200-29771400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr22:29765200-29769600	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr22:29765400-29776000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr22:29765400-29782600	Weak transcription	Colon Smooth Muscle	Colon
35	chr22:29765400-29783600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr22:29765600-29771000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr22:29765600-29771400	Weak transcription	HepG2	liver
38	chr22:29765600-29775800	Weak transcription	HUVEC	blood vessel
39	chr22:29765600-29783600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr22:29765600-29783600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:29765800-29771400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr22:29765800-29771400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr22:29765800-29771600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr22:29765800-29771800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr22:29765800-29772000	Weak transcription	NH-A	brain
46	chr22:29765800-29772600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr22:29765800-29778600	Weak transcription	A549	lung
48	chr22:29765800-29782800	Weak transcription	NHDF-Ad	bronchial
49	chr22:29766000-29770400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr22:29766000-29771600	Weak transcription	Adipose Nuclei	Adipose

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