Variant report

Variant	rs7689541
Chromosome Location	chr4:119506139-119506140
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: 49 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10004322	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031029	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[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]
rs11945703	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs12331454	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12648682	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12648778	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13115157	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13124091	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13137401	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146440	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs13146816	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs2029399	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2046779	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs2389780	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2728403	0.85[EUR][1000 genomes]
rs2787191	0.89[EUR][1000 genomes]
rs28448851	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs298998	0.89[YRI][hapmap]
rs3087958	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs35183273	0.80[EUR][1000 genomes]
rs35890030	0.98[ASN][1000 genomes]
rs3733517	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4001330	0.87[ASN][1000 genomes]
rs67276048	0.83[EUR][1000 genomes]
rs67655207	0.82[EUR][1000 genomes]
rs6813357	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6821350	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6833597	0.81[AMR][1000 genomes]
rs6836005	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs6847706	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs6857285	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs71241793	0.81[EUR][1000 genomes]
rs71610209	0.87[ASN][1000 genomes]
rs72676188	0.96[ASN][1000 genomes]
rs7653962	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7656990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669896	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs7692721	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7695602	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs9760578	0.81[AMR][1000 genomes];0.82[EUR][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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs7689541	RP11-384K6.6	cis	lung	GTEx
rs7689541	RP11-384K6.2	cis	Esophagus Mucosa	GTEx
rs7689541	RP11-384K6.6	cis	Nerve Tibial	GTEx
rs7689541	RP11-384K6.2	cis	Whole Blood	GTEx
rs7689541	RP11-384K6.2	cis	Artery Tibial	GTEx
rs7689541	RP11-384K6.6	cis	Esophagus Mucosa	GTEx
rs7689541	METTL14	cis	lymphoblastoid	seeQTL
rs7689541	RP11-384K6.2	cis	Adipose Subcutaneous	GTEx
rs7689541	RP11-384K6.6	cis	Adipose Subcutaneous	GTEx
rs7689541	RP11-384K6.2	cis	Thyroid	GTEx
rs7689541	RP11-384K6.2	cis	lung	GTEx
rs7689541	RP11-384K6.6	cis	Esophagus Muscularis	GTEx
rs7689541	RP11-384K6.6	cis	Skin Sun Exposed Lower leg	GTEx
rs7689541	RP11-384K6.6	cis	Artery Tibial	GTEx
rs7689541	RP11-384K6.6	cis	Thyroid	GTEx
rs7689541	RP11-384K6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7689541	RP11-384K6.6	cis	Whole Blood	GTEx
rs7689541	PRSS12	cis	parietal	SCAN
rs7689541	RP11-384K6.2	cis	Nerve Tibial	GTEx

Chromatin state (count:18 , 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	chr4:119505800-119506200	Enhancers	GM12878-XiMat	blood
5	chr4:119505800-119506800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:119505800-119506800	Enhancers	Ovary	ovary
7	chr4:119505800-119507000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr4:119505800-119507800	Enhancers	Duodenum Mucosa	Duodenum
9	chr4:119506000-119506200	Bivalent Enhancer	NHDF-Ad	bronchial
10	chr4:119506000-119506400	Enhancers	Fetal Muscle Trunk	muscle
11	chr4:119506000-119506400	Enhancers	Fetal Muscle Leg	muscle
12	chr4:119506000-119506400	Enhancers	Left Ventricle	heart
13	chr4:119506000-119506600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:119506000-119506600	Weak transcription	Hela-S3	cervix
15	chr4:119506000-119506800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr4:119506000-119506800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr4:119506000-119506800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:119506000-119508000	Enhancers	Pancreas	Pancrea

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