Variant report

Variant	rs12500353
Chromosome Location	chr4:110531351-110531352
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10004265	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017233	0.84[EUR][1000 genomes]
rs10027051	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149801	0.87[ASN][1000 genomes]
rs197205	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197208	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs197210	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs197211	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197212	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197214	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197215	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs197217	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197227	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533437	0.81[EUR][1000 genomes]
rs6533439	0.81[EUR][1000 genomes]
rs6533440	0.81[EUR][1000 genomes]
rs6533441	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6810809	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818852	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6827415	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6832174	0.84[EUR][1000 genomes]
rs6841003	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841563	0.93[EUR][1000 genomes]
rs9993676	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv3419480	chr4:110521397-110549622	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110529000-110533200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:110529800-110531600	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr4:110530000-110531400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:110530000-110531600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:110530000-110531600	Enhancers	Placenta	Placenta
6	chr4:110530000-110532000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr4:110530000-110532600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr4:110530600-110531600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr4:110530600-110533400	ZNF genes & repeats	Primary B cells from cord blood	blood
10	chr4:110530800-110531400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:110530800-110531400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:110530800-110531400	Enhancers	Right Atrium	heart
13	chr4:110530800-110531400	Genic enhancers	Spleen	Spleen
14	chr4:110530800-110531600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
15	chr4:110530800-110531600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:110530800-110532800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:110530800-110535600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:110531000-110531400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr4:110531000-110531600	Strong transcription	Thymus	Thymus
20	chr4:110531000-110531600	ZNF genes & repeats	Dnd41	blood
21	chr4:110531000-110531800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr4:110531000-110532000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr4:110531000-110532400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:110531000-110532600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:110531000-110532600	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr4:110531000-110532600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr4:110531000-110532600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr4:110531000-110532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:110531000-110546000	Weak transcription	Esophagus	oesophagus
30	chr4:110531000-110550600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:110531200-110531400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:110531200-110531600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:110531200-110531800	ZNF genes & repeats	Fetal Thymus	thymus
34	chr4:110531200-110533000	Enhancers	Monocytes-CD14+_RO01746	blood

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