Variant report

Variant	rs1961636
Chromosome Location	chr3:78802800-78802801
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	chr3:78789518..78792009-chr3:78800854..78802934,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11923155	0.82[ASN][1000 genomes]
rs1457659	0.82[EUR][1000 genomes]
rs17311036	0.83[ASN][1000 genomes]
rs17311057	0.83[ASN][1000 genomes]
rs17311169	0.83[ASN][1000 genomes]
rs17375739	0.83[EUR][1000 genomes]
rs17376753	0.83[ASN][1000 genomes]
rs1865860	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1865861	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865863	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333483	0.83[ASN][1000 genomes]
rs333506	0.83[ASN][1000 genomes]
rs333507	0.83[ASN][1000 genomes]
rs35077320	0.88[ASN][1000 genomes]
rs3773231	0.83[EUR][1000 genomes]
rs3773234	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773239	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773240	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773245	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821602	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821603	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56077922	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57046576	0.88[ASN][1000 genomes]
rs58423115	0.89[EUR][1000 genomes]
rs58792018	0.83[ASN][1000 genomes]
rs59263997	0.88[ASN][1000 genomes]
rs61053911	0.81[EUR][1000 genomes]
rs6548595	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66496525	0.88[ASN][1000 genomes]
rs66528054	0.88[ASN][1000 genomes]
rs67488304	0.82[ASN][1000 genomes]
rs67703869	0.88[ASN][1000 genomes]
rs72892461	0.88[ASN][1000 genomes]
rs72892501	0.83[ASN][1000 genomes]
rs73109772	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73109774	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73113488	0.87[ASN][1000 genomes]
rs73848602	0.83[ASN][1000 genomes]
rs7650002	0.83[ASN][1000 genomes]
rs9861603	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9866912	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv2753211	chr3:78784269-78809116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78783800-78803400	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:78787400-78802800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:78787400-78814800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:78788400-78803400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:78793600-78802800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:78796400-78803200	Weak transcription	HepG2	liver
7	chr3:78798600-78810200	Weak transcription	Fetal Lung	lung
8	chr3:78800800-78802800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:78801200-78802800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:78801200-78803200	Weak transcription	NHEK	skin
11	chr3:78801800-78804000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:78802200-78803200	Enhancers	Brain Hippocampus Middle	brain
13	chr3:78802200-78810200	Weak transcription	Fetal Stomach	stomach
14	chr3:78802400-78802800	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:78802400-78803800	Enhancers	Brain Anterior Caudate	brain
16	chr3:78802400-78804000	Enhancers	Brain Substantia Nigra	brain
17	chr3:78802400-78804200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:78802400-78804200	Enhancers	HMEC	breast
19	chr3:78802400-78804400	Enhancers	Hela-S3	cervix
20	chr3:78802400-78804600	Enhancers	Brain Angular Gyrus	brain
21	chr3:78802600-78803000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:78802600-78803200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr3:78802600-78803600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:78802600-78803800	Enhancers	NH-A	brain
25	chr3:78802600-78804000	Enhancers	Osteobl	bone
26	chr3:78802600-78804200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:78802600-78804600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:78802800-78803000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:78802800-78803000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:78802800-78803000	Enhancers	Pancreas	Pancrea
31	chr3:78802800-78803200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:78802800-78803200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:78802800-78803600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:78802800-78803600	Enhancers	HSMMtube	muscle
35	chr3:78802800-78803800	Enhancers	NHLF	lung
36	chr3:78802800-78804000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:78802800-78804000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:78802800-78804000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:78802800-78804200	Enhancers	Muscle Satellite Cultured Cells	--

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