Variant report

Variant	rs61490942
Chromosome Location	chr3:78888845-78888846
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	chr3:78887158..78889804-chr3:78895316..78898187,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12330873	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167944	1.00[ASN][1000 genomes]
rs28493625	1.00[EUR][1000 genomes]
rs28722753	1.00[EUR][1000 genomes]
rs331133	1.00[ASN][1000 genomes]
rs333501	1.00[ASN][1000 genomes]
rs57657065	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61270372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788270	1.00[EUR][1000 genomes]
rs72894427	0.85[AMR][1000 genomes]
rs72894434	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894439	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894449	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894451	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894453	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894457	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894459	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894460	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894461	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894463	1.00[ASN][1000 genomes]
rs72894464	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894467	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894471	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894474	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72894482	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72894501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896405	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	1.00[EUR][1000 genomes]
rs72904252	1.00[EUR][1000 genomes]
rs72904254	1.00[EUR][1000 genomes]
rs72904257	1.00[EUR][1000 genomes]
rs72904261	1.00[EUR][1000 genomes]
rs72906145	1.00[EUR][1000 genomes]
rs9808917	1.00[EUR][1000 genomes]
rs9813971	1.00[EUR][1000 genomes]
rs9817408	1.00[EUR][1000 genomes]
rs9818374	1.00[EUR][1000 genomes]
rs9831603	1.00[EUR][1000 genomes]
rs9847098	1.00[EUR][1000 genomes]
rs9872429	1.00[EUR][1000 genomes]
rs9876641	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78882000-78894800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:78886200-78895800	Weak transcription	NHLF	lung
3	chr3:78887200-78893000	Enhancers	HepG2	liver
4	chr3:78887400-78889400	Enhancers	Hela-S3	cervix
5	chr3:78887800-78889400	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr3:78887800-78896000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:78888800-78889000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:78888800-78889000	Enhancers	Fetal Lung	lung
9	chr3:78888800-78889200	Active TSS	A549	lung
10	chr3:78888800-78889400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:78888800-78889400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:78888800-78889400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:78888800-78889400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:78888800-78889400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:78888800-78889400	Enhancers	Brain Angular Gyrus	brain
16	chr3:78888800-78889400	Enhancers	Brain Hippocampus Middle	brain
17	chr3:78888800-78889400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:78888800-78889400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:78888800-78889400	Enhancers	HSMM	muscle
20	chr3:78888800-78889400	Enhancers	HUVEC	blood vessel
21	chr3:78888800-78889400	Enhancers	NH-A	brain
22	chr3:78888800-78889400	Enhancers	NHDF-Ad	bronchial
23	chr3:78888800-78889400	Enhancers	Osteobl	bone
24	chr3:78888800-78889600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:78888800-78889800	Enhancers	Brain Substantia Nigra	brain

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