Variant report

Variant	rs1992040
Chromosome Location	chr3:24581598-24581599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24578355..24581904-chr3:24581941..24583831,3	K562	blood:
2	chr3:24537190..24539322-chr3:24581064..24583038,2	K562	blood:
3	chr3:24559612..24561151-chr3:24581369..24583812,2	K562	blood:
4	chr3:24578631..24583271-chr3:24586680..24589577,4	K562	blood:
5	chr3:24560816..24563184-chr3:24580697..24582774,2	K562	blood:

Variant related genes	Relation type
ENSG00000265028	Chromatin interaction
ENSG00000228791	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10212332	0.84[ASN][1000 genomes]
rs10490837	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs11708042	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11712286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13318800	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561079	0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs17014900	0.87[CHB][hapmap];0.86[EUR][1000 genomes]
rs17014902	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[EUR][1000 genomes]
rs17029611	0.81[ASN][1000 genomes]
rs1992041	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2117873	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2117874	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2196434	0.85[ASN][1000 genomes]
rs2196435	0.85[CEU][hapmap]
rs2196438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28562279	0.82[EUR][1000 genomes]
rs3919672	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs56268655	0.87[EUR][1000 genomes]
rs58152527	0.86[ASN][1000 genomes]
rs61701305	0.86[ASN][1000 genomes]
rs6550878	0.88[ASN][1000 genomes]
rs6550879	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6767534	0.96[ASN][1000 genomes]
rs6767717	0.85[ASN][1000 genomes]
rs6769209	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6770518	0.86[ASN][1000 genomes]
rs6771818	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6781066	0.88[ASN][1000 genomes]
rs6795607	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6801494	0.85[ASN][1000 genomes]
rs73038411	0.87[EUR][1000 genomes]
rs73038427	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73040438	0.85[EUR][1000 genomes]
rs73040440	0.81[EUR][1000 genomes]
rs7647700	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930317	0.85[ASN][1000 genomes]
rs9310745	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9819865	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9823545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9835497	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843609	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844544	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9850781	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853927	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9859978	0.85[ASN][1000 genomes]
rs9861129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868375	0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9873830	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9878606	0.84[JPT][hapmap];0.85[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	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24566200-24591800	Weak transcription	Psoas Muscle	Psoas
2	chr3:24578000-24581600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:24580600-24581800	Weak transcription	Fetal Lung	lung
4	chr3:24580600-24582600	Enhancers	Colon Smooth Muscle	Colon
5	chr3:24580800-24581800	Weak transcription	Aorta	Aorta
6	chr3:24580800-24586400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:24580800-24587200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:24581000-24582000	Weak transcription	Fetal Heart	heart

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