Variant report

Variant	rs3829169
Chromosome Location	chr10:54044262-54044263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:54040036..54043559-chr10:54043700..54046471,3	K562	blood:
2	chr10:54044177..54046280-chr10:54072704..54074572,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236671	Chromatin interaction
ENSG00000107984	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10824270	0.86[EUR][1000 genomes]
rs10824297	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10824310	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10824321	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11001376	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11001389	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11001394	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11001421	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11001431	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11001455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11001457	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11001460	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194518	0.86[EUR][1000 genomes]
rs12569472	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16928725	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16928871	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3793783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898630	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57197814	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57497780	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58198087	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7085534	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7086430	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7101052	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787323	0.86[EUR][1000 genomes]
rs72787326	0.86[EUR][1000 genomes]
rs72787330	0.86[EUR][1000 genomes]
rs72787333	0.81[AMR][1000 genomes]
rs72787341	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7918883	0.81[AMR][1000 genomes];0.86[EUR][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	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv895399	chr10:53900872-54219820	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv550889	chr10:54016062-54044615	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54017400-54049600	Weak transcription	Left Ventricle	heart
2	chr10:54028000-54045600	Weak transcription	NHDF-Ad	bronchial
3	chr10:54029800-54055400	Weak transcription	Fetal Lung	lung
4	chr10:54036000-54050400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:54036800-54047400	Weak transcription	Fetal Intestine Large	intestine
6	chr10:54037800-54056000	Weak transcription	Fetal Muscle Leg	muscle
7	chr10:54040400-54044600	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:54040600-54057000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr10:54040800-54045400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:54041000-54048600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:54041400-54068200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:54042000-54044600	Weak transcription	Adipose Nuclei	Adipose
13	chr10:54042800-54068200	Weak transcription	Aorta	Aorta
14	chr10:54043000-54044600	Weak transcription	Psoas Muscle	Psoas
15	chr10:54043200-54044400	Weak transcription	HSMMtube	muscle
16	chr10:54043200-54047800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:54043200-54054600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:54043200-54060400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr10:54043200-54067800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:54043400-54044400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:54043600-54047200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr10:54044200-54045000	Enhancers	Primary B cells from peripheral blood	blood
23	chr10:54044200-54045000	Strong transcription	Fetal Muscle Trunk	muscle

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