Variant report

Variant	rs4729601
Chromosome Location	chr7:100251141-100251142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100249425..100251826-chr7:100281638..100283397,2	MCF-7	breast:
2	chr7:100249476..100251370-chr7:100270921..100272779,2	MCF-7	breast:
3	chr7:100250951..100252742-chr7:100270895..100272955,2	K562	blood:

Variant related genes	Relation type
ENSG00000146830	Chromatin interaction
ENSG00000172354	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10487157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs10953299	0.95[EUR][1000 genomes]
rs10953301	0.81[CHB][hapmap]
rs11520986	0.81[CHB][hapmap]
rs11764045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs11766643	0.89[AMR][1000 genomes]
rs11767547	0.91[AMR][1000 genomes]
rs11770389	0.89[AMR][1000 genomes]
rs11770534	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11772667	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11974395	0.81[CHB][hapmap]
rs11983745	0.91[AMR][1000 genomes]
rs12532878	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2075672	0.86[JPT][hapmap]
rs2075674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs2231170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2231172	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2272572	0.81[CHB][hapmap]
rs41303510	0.89[AMR][1000 genomes]
rs4727459	0.81[CHB][hapmap]
rs4729597	0.86[JPT][hapmap]
rs4729602	0.81[CHB][hapmap]
rs62482238	0.81[AMR][1000 genomes]
rs62482242	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6952341	0.88[EUR][1000 genomes]
rs6958696	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6969584	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6969697	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs73156234	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73170760	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73407376	0.81[AMR][1000 genomes]
rs7385804	0.86[JPT][hapmap]
rs7786877	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7812123	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7812235	0.89[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv607934	chr7:100240505-100271521	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4729601	PERQ1	Cis_1M	lymphoblastoid	RTeQTL
rs4729601	MOSPD3	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100238400-100252600	Weak transcription	Gastric	stomach
2	chr7:100241000-100253200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:100241600-100252400	Weak transcription	Brain Angular Gyrus	brain
4	chr7:100248200-100252400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr7:100248200-100252400	Weak transcription	Fetal Brain Female	brain
6	chr7:100249800-100252600	Weak transcription	Brain Germinal Matrix	brain
7	chr7:100250800-100251400	Enhancers	Placenta	Placenta
8	chr7:100250800-100251600	Enhancers	Hela-S3	cervix
9	chr7:100250800-100251600	Enhancers	HepG2	liver
10	chr7:100251000-100251200	Enhancers	Liver	Liver
11	chr7:100251000-100251200	Bivalent Enhancer	Stomach Mucosa	stomach

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