Variant report

Variant	rs7846145
Chromosome Location	chr8:87106710-87106711
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr8:87106676-87106740	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:87099204..87102058-chr8:87106597..87109469,2	MCF-7	breast:
2	chr8:87104968..87107537-chr8:87108407..87111374,2	MCF-7	breast:

Variant related genes	Relation type
ATP6V0D2	TF binding region
ENSG00000147614	Chromatin interaction
ENSG00000147613	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10098631	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10099368	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10102252	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10103166	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10106391	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10106497	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10107781	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10112076	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10504819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10955870	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11988449	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12682430	0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13257877	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs13260768	0.80[ASN][1000 genomes]
rs13267067	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs13274057	0.83[ASN][1000 genomes]
rs13281890	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1351777	0.83[ASN][1000 genomes]
rs1384878	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1384879	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1483765	0.95[ASN][1000 genomes]
rs16881545	0.83[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16883602	0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16887456	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1872135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1968869	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2220106	0.96[ASN][1000 genomes]
rs2318396	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2318936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2873692	0.80[ASN][1000 genomes]
rs35910910	0.87[ASN][1000 genomes]
rs4370510	0.94[ASN][1000 genomes]
rs4960948	0.96[ASN][1000 genomes]
rs4960953	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4960954	0.84[ASN][1000 genomes]
rs4960955	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4960959	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4961065	0.88[YRI][hapmap]
rs4961068	0.86[CHB][hapmap]
rs4961071	0.96[ASN][1000 genomes]
rs4961072	0.90[ASN][1000 genomes]
rs4961074	0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4961075	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4961077	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4961078	0.87[ASN][1000 genomes]
rs4961092	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs57651622	0.96[ASN][1000 genomes]
rs57962008	0.96[ASN][1000 genomes]
rs58243820	0.96[ASN][1000 genomes]
rs59028033	0.96[ASN][1000 genomes]
rs60506092	0.88[ASN][1000 genomes]
rs61629815	0.96[ASN][1000 genomes]
rs62509924	0.95[ASN][1000 genomes]
rs62509930	0.96[ASN][1000 genomes]
rs62509933	0.94[ASN][1000 genomes]
rs6469703	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6981194	0.89[ASN][1000 genomes]
rs6993377	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7000491	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7001674	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7001699	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7005999	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7016268	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7813508	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7821560	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7831328	0.89[ASN][1000 genomes]
rs7836003	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7837251	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs9643132	0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9643143	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9643144	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428204	chr8:86405478-87312208	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv529563	chr8:86467090-87381984	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv1028959	chr8:86835367-87142383	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv891147	chr8:86886950-87333968	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1034721	chr8:86977250-87131151	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv891148	chr8:86987886-87149808	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv891149	chr8:87023306-87167184	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1034855	chr8:87040075-87168730	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	esv3493409	chr8:87085885-87109161	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	esv3493410	chr8:87085885-87109161	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv611673	chr8:87106710-87136320	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7846145	RALYL	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87082400-87126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:87106200-87108000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:87106400-87110800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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