Variant report

Variant	rs2389780
Chromosome Location	chr4:119506680-119506681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119505891..119507633-chr4:119509359..119512309,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10004322	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022024	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031029	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10857060	1.00[ASN][1000 genomes]
rs11728902	0.84[EUR][1000 genomes]
rs11734153	1.00[ASN][1000 genomes]
rs12331454	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13137401	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2728403	0.83[EUR][1000 genomes]
rs2787191	0.87[EUR][1000 genomes]
rs28448851	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35890030	0.98[ASN][1000 genomes]
rs4001330	0.87[ASN][1000 genomes]
rs67276048	0.81[EUR][1000 genomes]
rs71241793	0.80[EUR][1000 genomes]
rs71610209	0.87[ASN][1000 genomes]
rs72676188	0.96[ASN][1000 genomes]
rs7656990	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669896	1.00[ASN][1000 genomes]
rs7689541	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv980150	chr4:119499004-119514502	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2389780	RP11-384K6.6	cis	Thyroid	GTEx
rs2389780	RP11-384K6.6	cis	Adipose Subcutaneous	GTEx
rs2389780	RP11-384K6.2	cis	Artery Tibial	GTEx
rs2389780	RP11-384K6.2	cis	lung	GTEx
rs2389780	RP11-384K6.6	cis	Esophagus Muscularis	GTEx
rs2389780	RP11-384K6.2	cis	Nerve Tibial	GTEx
rs2389780	RP11-384K6.6	cis	Whole Blood	GTEx
rs2389780	RP11-384K6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2389780	RP11-384K6.6	cis	Skin Sun Exposed Lower leg	GTEx
rs2389780	RP11-384K6.6	cis	lung	GTEx
rs2389780	RP11-384K6.2	cis	Thyroid	GTEx
rs2389780	RP11-384K6.6	cis	Nerve Tibial	GTEx
rs2389780	RP11-384K6.6	cis	Artery Tibial	GTEx
rs2389780	RP11-384K6.2	cis	Whole Blood	GTEx
rs2389780	RP11-384K6.6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119504000-119507000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:119505200-119506800	Enhancers	K562	blood
3	chr4:119505600-119506800	Enhancers	Liver	Liver
4	chr4:119505800-119506800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:119505800-119506800	Enhancers	Ovary	ovary
6	chr4:119505800-119507000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr4:119505800-119507800	Enhancers	Duodenum Mucosa	Duodenum
8	chr4:119506000-119506800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr4:119506000-119506800	Enhancers	H9 Cell Line	embryonic stem cell
10	chr4:119506000-119506800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:119506000-119508000	Enhancers	Pancreas	Pancrea
12	chr4:119506400-119506800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:119506400-119506800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr4:119506400-119507400	Enhancers	Stomach Mucosa	stomach
15	chr4:119506400-119507800	Enhancers	Placenta	Placenta
16	chr4:119506400-119508000	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr4:119506600-119506800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr4:119506600-119506800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr4:119506600-119506800	Enhancers	Osteobl	bone
20	chr4:119506600-119507000	Enhancers	Left Ventricle	heart
21	chr4:119506600-119507200	Enhancers	Hela-S3	cervix
22	chr4:119506600-119507400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr4:119506600-119508000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr4:119506600-119512800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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