Variant report

Variant	rs487882
Chromosome Location	chr9:18726694-18726695
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	chr9:18725510..18728390-chr9:18733590..18735848,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs2507117	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2779124	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779127	0.81[ASW][hapmap]
rs476460	0.85[ASN][1000 genomes]
rs480335	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs482009	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs484122	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs502981	0.84[AMR][1000 genomes]
rs507556	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs518607	0.94[CHD][hapmap]
rs519115	0.91[AMR][1000 genomes]
rs519878	0.91[AMR][1000 genomes]
rs521546	1.00[ASW][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs521911	0.93[ASW][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs530120	0.88[CHD][hapmap];0.85[MEX][hapmap]
rs531847	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs532101	0.81[ASN][1000 genomes]
rs532543	0.82[ASN][1000 genomes]
rs542826	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs542956	0.91[AMR][1000 genomes]
rs547927	0.85[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs563805	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs574090	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs574151	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs580568	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs776569	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv892691	chr9:18519699-18805483	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv831523	chr9:18592398-18753451	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv892694	chr9:18599029-18767830	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv892697	chr9:18700566-18767830	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs487882	MYL3	trans	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18708800-18727000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr9:18710400-18756400	Weak transcription	HSMMtube	muscle
3	chr9:18721800-18739800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:18721800-18740200	Strong transcription	Osteobl	bone
5	chr9:18721800-18745800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:18723200-18740000	Weak transcription	Aorta	Aorta
7	chr9:18723400-18728600	Weak transcription	NHLF	lung
8	chr9:18723400-18731200	Strong transcription	HSMM	muscle
9	chr9:18723800-18745800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:18724000-18727800	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr9:18725600-18727000	Weak transcription	NH-A	brain
12	chr9:18726000-18727200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:18726200-18727200	Enhancers	Rectal Smooth Muscle	rectum
14	chr9:18726200-18727600	Enhancers	NHDF-Ad	bronchial
15	chr9:18726200-18729600	Enhancers	Fetal Stomach	stomach
16	chr9:18726400-18726800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:18726400-18726800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:18726400-18726800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:18726400-18727400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:18726400-18727600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:18726400-18727600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr9:18726400-18727600	Enhancers	Fetal Intestine Large	intestine
23	chr9:18726400-18727600	Enhancers	Fetal Muscle Leg	muscle
24	chr9:18726400-18729200	Enhancers	Colon Smooth Muscle	Colon
25	chr9:18726600-18726800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:18726600-18727000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:18726600-18727400	Enhancers	Adipose Nuclei	Adipose
28	chr9:18726600-18727400	Enhancers	Fetal Heart	heart
29	chr9:18726600-18727600	Enhancers	Fetal Kidney	kidney
30	chr9:18726600-18727600	Enhancers	Fetal Lung	lung

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