Variant report

Variant	rs1920375
Chromosome Location	chr3:115855619-115855620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10804521	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10804522	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12488904	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12496701	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1381065	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1461110	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1461112	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1461113	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1461138	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1563933	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16824478	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16824491	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17631108	1.00[ASN][1000 genomes]
rs17698500	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17699134	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs1920363	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1920365	0.94[ASN][1000 genomes]
rs1920367	0.94[ASN][1000 genomes]
rs1920370	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1950085	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2141628	0.92[ASN][1000 genomes]
rs41456847	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4146782	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4261878	0.94[ASN][1000 genomes]
rs4511899	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4560296	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57196061	0.94[ASN][1000 genomes]
rs57425502	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62269187	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6779886	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6787788	1.00[CHB][hapmap]
rs73140910	1.00[ASN][1000 genomes]
rs73140911	1.00[ASN][1000 genomes]
rs73140912	1.00[ASN][1000 genomes]
rs73140913	1.00[ASN][1000 genomes]
rs73140921	0.94[ASN][1000 genomes]
rs7428913	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7614089	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7639609	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115851400-115858400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:115853200-115855800	Enhancers	Rectal Smooth Muscle	rectum
3	chr3:115853200-115856200	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:115853400-115856000	Enhancers	Colon Smooth Muscle	Colon
5	chr3:115853400-115859000	Enhancers	Brain Substantia Nigra	brain
6	chr3:115853600-115856400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:115853800-115855800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:115854000-115856000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:115854000-115857000	Enhancers	Brain Angular Gyrus	brain
10	chr3:115854000-115858400	Enhancers	Brain Hippocampus Middle	brain
11	chr3:115854200-115857000	Enhancers	Brain Cingulate Gyrus	brain
12	chr3:115854200-115861200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:115854800-115858400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:115854800-115860400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:115855000-115856200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:115855000-115856800	Enhancers	Brain Anterior Caudate	brain
17	chr3:115855000-115857000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:115855200-115857000	Enhancers	Brain Germinal Matrix	brain
19	chr3:115855200-115858000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:115855200-115858400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:115855200-115860800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:115855200-115864200	Weak transcription	Fetal Lung	lung

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