Variant report

Variant	rs4572006
Chromosome Location	chr5:49900981-49900982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49900480..49902241-chr5:49904940..49907468,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10044566	1.00[CHB][hapmap]
rs10050585	0.84[ASN][1000 genomes]
rs10055793	0.84[ASN][1000 genomes]
rs10056836	1.00[CHB][hapmap]
rs10057335	0.84[ASN][1000 genomes]
rs10059085	1.00[CHB][hapmap]
rs10075034	1.00[CHB][hapmap]
rs10461587	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10471915	0.84[ASN][1000 genomes]
rs10755235	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10940423	0.86[ASN][1000 genomes]
rs10940424	0.83[ASN][1000 genomes]
rs10940425	0.88[EUR][1000 genomes]
rs10940497	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11738761	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11745945	1.00[ASN][1000 genomes]
rs11750771	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12188262	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12188654	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12653803	0.88[ASN][1000 genomes]
rs13355434	0.89[EUR][1000 genomes]
rs13356533	0.88[ASN][1000 genomes]
rs154137	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs154138	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16879103	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs16884018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs169497	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs182230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1839128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1900738	0.88[ASN][1000 genomes]
rs1972980	0.92[ASN][1000 genomes]
rs2034393	1.00[ASN][1000 genomes]
rs2121979	1.00[ASN][1000 genomes]
rs2166893	1.00[ASN][1000 genomes]
rs2166894	1.00[ASN][1000 genomes]
rs2354526	0.84[ASN][1000 genomes]
rs2548581	0.85[CHB][hapmap]
rs2548582	1.00[JPT][hapmap]
rs256340	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs256341	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2594706	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26065	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26069	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26071	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs27466	0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs27467	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs27468	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs27469	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs27627	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs282550	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs282553	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs282561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs28810787	0.84[ASN][1000 genomes]
rs32376	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs32425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35167447	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35667121	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs42284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4282859	0.92[ASN][1000 genomes]
rs4440312	0.92[ASN][1000 genomes]
rs4865628	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4865894	0.89[EUR][1000 genomes]
rs4865895	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4865896	0.93[AFR][1000 genomes]
rs56052855	0.82[AMR][1000 genomes]
rs6450292	0.88[ASN][1000 genomes]
rs6450301	0.84[ASN][1000 genomes]
rs6863162	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863575	0.89[ASN][1000 genomes]
rs6867590	0.89[ASN][1000 genomes]
rs6868550	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6869906	0.81[EUR][1000 genomes]
rs6872070	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6872496	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6883718	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6887758	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890519	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6890869	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6893665	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7702541	0.88[ASN][1000 genomes]
rs7721050	0.92[ASN][1000 genomes]
rs7725954	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs7736142	0.88[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	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv964850	chr5:49883635-49942856	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv14399	chr5:49885912-49934455	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4572006	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs4572006	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49896000-49903400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:49898200-49902000	Weak transcription	Hela-S3	cervix

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