Variant report

Variant	rs28412170
Chromosome Location	chr4:53438426-53438427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10000311	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10001085	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10001370	0.94[ASN][1000 genomes]
rs10001387	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10002261	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10003396	0.81[ASN][1000 genomes]
rs10010306	1.00[ASN][1000 genomes]
rs10012676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10014752	0.93[ASN][1000 genomes]
rs10014850	0.87[ASN][1000 genomes]
rs10020568	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10021143	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10023867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10027906	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10028085	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10028755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10029145	1.00[ASN][1000 genomes]
rs10031386	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10032700	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10033218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10471216	0.93[ASN][1000 genomes]
rs13434726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13435157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28376189	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28376284	1.00[AFR][1000 genomes]
rs28379922	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28380682	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28396506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402205	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28411005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28430452	0.93[ASN][1000 genomes]
rs28436702	0.87[AFR][1000 genomes]
rs28451750	1.00[ASN][1000 genomes]
rs28475600	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28478374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28482298	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28503210	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28514875	1.00[AFR][1000 genomes]
rs28565016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28588481	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28590396	0.93[ASN][1000 genomes]
rs28619184	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28644292	1.00[ASN][1000 genomes]
rs28651623	1.00[AFR][1000 genomes]
rs28654693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28660550	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28660571	0.93[ASN][1000 genomes]
rs28672279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28694544	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28711292	1.00[AFR][1000 genomes]
rs28721897	0.93[ASN][1000 genomes]
rs28722174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28784684	0.93[ASN][1000 genomes]
rs28825181	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28825412	0.93[ASN][1000 genomes]
rs28849759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28852068	0.93[ASN][1000 genomes]
rs6830833	0.93[ASN][1000 genomes]
rs7673679	0.90[ASN][1000 genomes]
rs9990686	0.93[ASN][1000 genomes]
rs9994643	0.93[ASN][1000 genomes]
rs9997863	0.93[ASN][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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv999397	chr4:53157525-53448384	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv482581	chr4:53310749-53480710	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS 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	25 gene(s)	inside rSNPs	diseases
5	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription 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	25 gene(s)	inside rSNPs	diseases
7	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53427600-53439000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:53427800-53438800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:53433200-53443800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:53434000-53441800	Weak transcription	Left Ventricle	heart
5	chr4:53434200-53443000	Weak transcription	Fetal Heart	heart
6	chr4:53435000-53440000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:53435400-53439200	Weak transcription	Right Atrium	heart
8	chr4:53435600-53438800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:53435800-53440000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:53436600-53440000	Enhancers	Placenta	Placenta
11	chr4:53436800-53439600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:53437800-53439400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:53438200-53439000	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:53438200-53440600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:53438400-53438800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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