Variant report

Variant	rs1378984
Chromosome Location	chr4:45651185-45651186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10016628	0.88[AMR][1000 genomes]
rs10024392	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10938410	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1350198	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1378981	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1378983	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1378985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1378989	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1456497	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1456499	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1456500	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1456501	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1456502	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1456506	0.84[AMR][1000 genomes]
rs1456507	0.84[AMR][1000 genomes]
rs1563479	0.95[EUR][1000 genomes]
rs1563480	0.95[EUR][1000 genomes]
rs1563481	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1840743	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1840744	0.95[EUR][1000 genomes]
rs1869981	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1902505	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1968749	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1993435	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2085383	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2124681	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124682	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2168540	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2168541	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4033830	0.95[EUR][1000 genomes]
rs4033831	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4513608	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4694810	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4695128	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6447466	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6814398	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6821525	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6825626	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6849927	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs727244	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7665999	0.95[EUR][1000 genomes]
rs7682261	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7682948	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7688109	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7695342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7696046	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994279	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997201	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594104	chr4:45105210-45665828	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv461353	chr4:45470453-46227847	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv470030	chr4:45470453-46227847	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594109	chr4:45470453-46227847	Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv461355	chr4:45483121-45982196	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv594111	chr4:45483121-45982196	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv594112	chr4:45503395-45756683	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv997267	chr4:45524521-45703126	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:45649200-45651200	Enhancers	Fetal Intestine Small	intestine
2	chr4:45649400-45651200	Enhancers	Fetal Intestine Large	intestine
3	chr4:45649600-45651600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr4:45650000-45652200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:45650200-45651200	Weak transcription	Stomach Mucosa	stomach
6	chr4:45650600-45651400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:45651000-45651400	Enhancers	Fetal Lung	lung

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