Variant report

Variant	rs479956
Chromosome Location	chr3:78967892-78967893
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78959136..78961059-chr3:78966267..78968537,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs13075210	0.81[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162262	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs162263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162264	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs162265	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs162266	0.92[ASN][1000 genomes]
rs162267	0.89[ASN][1000 genomes]
rs162268	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs162425	0.90[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs162426	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs162427	0.82[EUR][1000 genomes]
rs162428	0.87[CHB][hapmap];0.82[EUR][1000 genomes]
rs162429	0.87[CEU][hapmap];0.93[CHB][hapmap];0.83[EUR][1000 genomes]
rs17313732	0.86[CHB][hapmap]
rs186648	0.83[EUR][1000 genomes]
rs186688	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs328045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs328047	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs329805	0.87[CHB][hapmap];0.80[EUR][1000 genomes]
rs329812	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs329813	0.80[CHB][hapmap]
rs329814	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs329815	0.90[ASN][1000 genomes]
rs329816	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs329817	0.89[ASN][1000 genomes]
rs329819	0.93[CHB][hapmap]
rs329822	0.94[CHB][hapmap]
rs329824	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs329825	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs331149	0.87[CEU][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs331158	0.86[CHB][hapmap]
rs331182	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs331183	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs331184	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs331188	0.81[EUR][1000 genomes]
rs331199	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs369346	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs379346	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs387900	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs388421	0.84[EUR][1000 genomes]
rs420481	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs425121	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs432141	0.86[ASN][1000 genomes]
rs434929	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs453354	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484531	0.84[EUR][1000 genomes]
rs498805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512135	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531125	0.87[CEU][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6548601	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs6772919	0.87[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs6800782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7617538	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7619765	0.86[EUR][1000 genomes];0.91[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	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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78959600-78987200	Weak transcription	Fetal Lung	lung
2	chr3:78963200-78991000	Weak transcription	Fetal Brain Male	brain
3	chr3:78966200-78972800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:78966800-78969000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:78966800-78969200	Enhancers	Osteobl	bone
6	chr3:78967000-78968000	Enhancers	Brain Angular Gyrus	brain
7	chr3:78967000-78968200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:78967000-78968200	Enhancers	Adipose Nuclei	Adipose
9	chr3:78967000-78969000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:78967000-78969000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:78967000-78969000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:78967000-78969000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:78967000-78969000	Enhancers	NHDF-Ad	bronchial
14	chr3:78967000-78969600	Enhancers	HepG2	liver
15	chr3:78967200-78968800	Enhancers	Hela-S3	cervix
16	chr3:78967200-78987200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:78967200-79000600	Weak transcription	Fetal Kidney	kidney
18	chr3:78967400-78968200	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr3:78967400-78969200	Enhancers	NHEK	skin
20	chr3:78967600-78968600	Enhancers	NHLF	lung
21	chr3:78967600-78968800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:78967800-78968600	Enhancers	Brain Hippocampus Middle	brain
23	chr3:78967800-78968800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:78967800-78968800	Enhancers	Colon Smooth Muscle	Colon
25	chr3:78967800-78968800	Enhancers	HSMM	muscle
26	chr3:78967800-78968800	Enhancers	NH-A	brain
27	chr3:78967800-78969000	Enhancers	HMEC	breast

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