Variant report

Variant	rs999415
Chromosome Location	chr5:116185049-116185050
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10035572	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10051070	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10051209	0.81[JPT][hapmap]
rs10053269	0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10053279	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10069564	0.87[ASN][1000 genomes]
rs10073924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035861	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs10463687	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10463688	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10478313	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241405	0.98[ASN][1000 genomes]
rs11956132	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515487	0.95[ASN][1000 genomes]
rs12515978	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12517201	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12519375	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175939	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1366158	0.84[ASN][1000 genomes]
rs1366159	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1428007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153582	0.94[ASN][1000 genomes]
rs153585	0.94[ASN][1000 genomes]
rs153586	0.94[ASN][1000 genomes]
rs1863966	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253895	0.92[ASN][1000 genomes]
rs253896	0.93[ASN][1000 genomes]
rs253897	0.94[ASN][1000 genomes]
rs253899	0.94[ASN][1000 genomes]
rs46588	0.92[ASN][1000 genomes]
rs722958	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527974	chr5:115987168-116303678	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv462403	chr5:115994775-116284378	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv599485	chr5:115994775-116284378	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1030056	chr5:116008971-116278725	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1033140	chr5:116035131-116314673	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1027701	chr5:116138286-116185586	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1020292	chr5:116183712-116349633	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116181000-116189800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:116181800-116186000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:116183400-116185600	Enhancers	HepG2	liver
4	chr5:116184600-116185600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:116184800-116185200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr5:116184800-116185200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:116184800-116185200	Enhancers	Fetal Muscle Leg	muscle
8	chr5:116185000-116185200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:116185000-116185200	Bivalent Enhancer	Fetal Intestine Large	intestine
10	chr5:116185000-116185200	Bivalent Enhancer	Fetal Intestine Small	intestine
11	chr5:116185000-116185400	Enhancers	Cortex derived primary cultured neurospheres	brain

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