Variant report

Variant	rs6788270
Chromosome Location	chr3:78939351-78939352
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12330873	1.00[EUR][1000 genomes]
rs28493625	1.00[EUR][1000 genomes]
rs28722753	1.00[EUR][1000 genomes]
rs61270372	1.00[EUR][1000 genomes]
rs61490942	1.00[EUR][1000 genomes]
rs72894482	1.00[EUR][1000 genomes]
rs72894501	1.00[EUR][1000 genomes]
rs72896405	1.00[EUR][1000 genomes]
rs72896408	1.00[EUR][1000 genomes]
rs72896421	1.00[EUR][1000 genomes]
rs72896425	1.00[EUR][1000 genomes]
rs72896439	1.00[EUR][1000 genomes]
rs72896443	1.00[EUR][1000 genomes]
rs72896444	1.00[EUR][1000 genomes]
rs72896497	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72904252	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72904254	1.00[EUR][1000 genomes]
rs72904257	1.00[EUR][1000 genomes]
rs72904261	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72906145	1.00[EUR][1000 genomes]
rs9808917	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813971	0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9817408	0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9818374	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831603	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9847098	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9849586	0.90[AMR][1000 genomes]
rs9872429	0.85[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9876641	1.00[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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590735	chr3:78922852-78977507	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78922600-78944000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:78923000-78943800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:78927600-78943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:78930400-78942200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:78930400-78944000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:78930600-78948600	Weak transcription	Fetal Lung	lung
7	chr3:78930800-78943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:78936800-78942000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:78937000-78943800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:78937000-78946000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:78937000-78946400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:78937200-78943800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:78937800-78942200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:78937800-78943800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:78938200-78953400	Weak transcription	HepG2	liver
16	chr3:78938800-78942200	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:78938800-78943000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:78938800-78943800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:78939000-78943800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:78939200-78943800	Weak transcription	Fetal Brain Male	brain

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