Variant report

Variant	rs16824478
Chromosome Location	chr3:115871591-115871592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10804521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10804522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12485667	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12486465	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12488904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12496701	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1381065	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs1461110	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1461112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1461113	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1461115	0.80[EUR][1000 genomes]
rs1461117	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1461138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1563933	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16824491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16824495	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17359	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17631108	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17643878	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17698500	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17699134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1920363	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920365	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920367	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920370	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1920375	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1950085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2141628	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34424845	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41456847	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4146782	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4261878	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4511899	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4560296	1.00[ASN][1000 genomes]
rs57196061	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57425502	1.00[ASN][1000 genomes]
rs62269187	1.00[ASN][1000 genomes]
rs62269188	0.84[ASN][1000 genomes]
rs62269190	0.84[ASN][1000 genomes]
rs67278926	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67551037	0.84[ASN][1000 genomes]
rs6779886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67853012	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6787788	0.90[CHB][hapmap]
rs73140910	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73140911	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73140912	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73140913	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73140921	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140968	0.82[EUR][1000 genomes]
rs7428913	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7614089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7639126	0.86[AMR][1000 genomes]
rs7639609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][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	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2751975	chr3:115766285-115902901	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2755046	chr3:115818840-115942952	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv591345	chr3:115819376-115902901	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2752728	chr3:115833212-115902901	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2751976	chr3:115867310-115903310	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115866800-115871600	Enhancers	Brain Germinal Matrix	brain
2	chr3:115868400-115872000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:115868600-115879600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:115868800-115872000	Weak transcription	Fetal Lung	lung
5	chr3:115869000-115880000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:115869200-115871600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:115869400-115874800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:115869600-115872000	Weak transcription	Brain Anterior Caudate	brain
9	chr3:115869800-115874600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:115870200-115873000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:115870200-115877000	Weak transcription	Brain Angular Gyrus	brain
12	chr3:115870400-115872000	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:115870400-115873200	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:115870800-115872400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:115871200-115872000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:115871200-115872400	Enhancers	Rectal Smooth Muscle	rectum
17	chr3:115871400-115871800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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