Variant report

Variant	rs299202
Chromosome Location	chr5:118303974-118303975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11241493	1.00[JPT][hapmap]
rs13170553	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs169917	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213435	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431601	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2431602	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2442123	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299191	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs299194	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299201	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299205	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299206	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299209	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299214	1.00[JPT][hapmap]
rs368569	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs411110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333791	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1017548	chr5:118276479-118358394	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv964930	chr5:118301974-118317943	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 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	chr5:118259600-118305000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr5:118263000-118306000	Weak transcription	Primary T cells from cord blood	blood
3	chr5:118263400-118304000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr5:118282200-118304200	Weak transcription	Right Atrium	heart
5	chr5:118294400-118304200	Weak transcription	Left Ventricle	heart
6	chr5:118296800-118314400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:118299400-118304600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:118299800-118304200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:118301000-118304200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:118301200-118304000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:118301800-118304000	Enhancers	Hela-S3	cervix
12	chr5:118302600-118304000	Enhancers	HepG2	liver
13	chr5:118302600-118304200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:118302800-118305000	Weak transcription	Pancreas	Pancrea
15	chr5:118303400-118304000	Weak transcription	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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