Variant report

Variant	rs4729606
Chromosome Location	chr7:100321790-100321791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100315279..100318194-chr7:100320126..100322658,3	K562	blood:
2	chr7:100315257..100318069-chr7:100320272..100323098,2	MCF-7	breast:
3	chr7:100319576..100322114-chr7:100397770..100400557,3	MCF-7	breast:
4	chr7:100288252..100292867-chr7:100319528..100322364,4	K562	blood:
5	chr7:100302553..100308135-chr7:100314195..100322207,16	MCF-7	breast:
6	chr7:100321531..100325332-chr7:100423998..100426364,3	MCF-7	breast:
7	chr7:100291635..100293380-chr7:100321369..100322955,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172336	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000146828	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10277087	0.89[JPT][hapmap]
rs10487157	0.80[MEX][hapmap]
rs10953300	0.87[EUR][1000 genomes]
rs10953301	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10953302	0.86[ASW][hapmap]
rs11520986	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs11760602	0.87[EUR][1000 genomes]
rs11764045	0.80[MEX][hapmap]
rs11765509	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11769012	0.92[EUR][1000 genomes]
rs11772052	0.92[EUR][1000 genomes]
rs11772849	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11973874	0.87[EUR][1000 genomes]
rs11974395	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs11979818	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs11980509	0.94[EUR][1000 genomes]
rs11983334	0.95[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs11984421	0.84[EUR][1000 genomes]
rs12531792	0.90[EUR][1000 genomes]
rs12532878	0.80[MEX][hapmap]
rs1734908	0.89[JPT][hapmap]
rs2075671	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs2075674	0.85[MEX][hapmap]
rs221790	0.89[JPT][hapmap]
rs221795	0.89[JPT][hapmap]
rs221801	0.89[JPT][hapmap]
rs2231172	0.84[ASW][hapmap];0.85[MEX][hapmap]
rs2272572	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2293769	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4727459	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs4729602	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs4729605	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4729607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504141	0.89[JPT][hapmap]
rs507392	0.89[JPT][hapmap]
rs551238	0.89[JPT][hapmap]
rs62482249	0.87[EUR][1000 genomes]
rs62482250	0.87[EUR][1000 genomes]
rs62482251	0.87[EUR][1000 genomes]
rs62482252	0.88[EUR][1000 genomes]
rs62483567	0.90[EUR][1000 genomes]
rs62483569	0.93[EUR][1000 genomes]
rs62483570	0.94[EUR][1000 genomes]
rs6942733	1.00[ASW][hapmap];0.85[CEU][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs6969584	0.80[MEX][hapmap]
rs6969697	0.80[MEX][hapmap]
rs7812123	0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
3	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
4	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
5	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
6	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
7	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	esv1804951	chr7:100275135-100374093	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv888796	chr7:100313420-100423365	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	esv1829284	chr7:100318927-100337055	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	esv3519627	chr7:100320350-100343994	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	esv3519628	chr7:100320350-100343994	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4729606	LHFPL3	cis	cerebellum	SCAN
rs4729606	BRI3	cis	cerebellum	SCAN
rs4729606	PERQ1	Cis_1M	lymphoblastoid	RTeQTL
rs4729606	TSC22D4	cis	parietal	SCAN
rs4729606	GIGYF1	cis	lymphoblastoid	seeQTL
rs4729606	MOSPD3	cis	Whole Blood	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100319200-100342800	Weak transcription	Right Atrium	heart
2	chr7:100320000-100322800	Weak transcription	Placenta	Placenta
3	chr7:100320200-100322800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:100320400-100321800	Flanking Active TSS	Pancreas	Pancrea
5	chr7:100320400-100322200	Flanking Active TSS	Liver	Liver
6	chr7:100321400-100322000	Flanking Active TSS	HepG2	liver

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