Variant report

Variant	rs10015198
Chromosome Location	chr4:601791-601792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:594354..601823-chr4:659072..674169,20	MCF-7	breast:
2	chr4:599560..602481-chr4:609054..611964,2	K562	blood:
3	chr1:115298950..115300909-chr4:600171..602025,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE6B-1	chr4:601762-601867	l_2578_chr4:572257-601867_testes

Variant related genes	Relation type
ENSG00000169020	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000215375	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10010598	0.87[MKK][hapmap];0.84[YRI][hapmap]
rs10012461	0.85[EUR][1000 genomes]
rs10017347	0.88[MKK][hapmap]
rs10018393	1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10020292	0.82[MKK][hapmap]
rs10024575	0.85[EUR][1000 genomes]
rs10027392	0.88[MKK][hapmap];0.84[YRI][hapmap]
rs10029924	0.88[MKK][hapmap];0.84[YRI][hapmap]
rs10030020	0.84[YRI][hapmap]
rs11726338	1.00[MEX][hapmap]
rs12331186	0.93[MKK][hapmap];0.84[YRI][hapmap]
rs13101691	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13103955	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13104878	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs13107526	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13110755	0.87[EUR][1000 genomes]
rs13111179	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13114299	0.87[EUR][1000 genomes]
rs13116523	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13117283	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13118033	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13127213	0.96[EUR][1000 genomes]
rs13133935	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13136626	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13139052	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13139089	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13143415	0.91[EUR][1000 genomes]
rs13147797	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13150119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28399001	0.88[MKK][hapmap];0.84[YRI][hapmap]
rs28510278	0.88[MKK][hapmap]
rs28510755	0.88[MKK][hapmap]
rs28531889	0.88[MKK][hapmap]
rs28538930	0.88[MKK][hapmap];0.84[YRI][hapmap]
rs28594284	0.88[MKK][hapmap];0.84[YRI][hapmap]
rs28648408	1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs28654405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28665728	0.82[MKK][hapmap];0.84[YRI][hapmap]
rs28682363	0.85[EUR][1000 genomes]
rs28687729	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28710261	0.87[AFR][1000 genomes]
rs28754934	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34053163	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34075612	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34094325	1.00[EUR][1000 genomes]
rs34096984	1.00[EUR][1000 genomes]
rs34165278	1.00[EUR][1000 genomes]
rs34293668	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34363025	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34366493	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34391278	1.00[EUR][1000 genomes]
rs34402770	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34421911	1.00[EUR][1000 genomes]
rs34477049	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34568772	1.00[EUR][1000 genomes]
rs34585712	1.00[EUR][1000 genomes]
rs34587191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34698095	1.00[EUR][1000 genomes]
rs34953355	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs34992186	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35006826	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35137658	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35158410	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35207129	1.00[EUR][1000 genomes]
rs35219160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35270524	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35455427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35535457	1.00[EUR][1000 genomes]
rs35564967	1.00[EUR][1000 genomes]
rs35621318	0.87[EUR][1000 genomes]
rs35621580	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35649145	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs35694609	1.00[EUR][1000 genomes]
rs35732782	1.00[EUR][1000 genomes]
rs35843044	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35853545	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35869797	1.00[EUR][1000 genomes]
rs35894204	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35896648	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35925646	0.87[EUR][1000 genomes]
rs35935310	1.00[EUR][1000 genomes]
rs35972513	1.00[EUR][1000 genomes]
rs36060793	1.00[EUR][1000 genomes]
rs36117387	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61760239	0.87[EUR][1000 genomes]
rs71602477	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602479	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602480	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602481	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602482	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602484	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602486	1.00[EUR][1000 genomes]
rs71602489	1.00[EUR][1000 genomes]
rs71602490	0.91[EUR][1000 genomes]
rs71602492	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602500	0.87[EUR][1000 genomes]
rs7657809	0.85[EUR][1000 genomes]
rs7665160	0.88[MKK][hapmap];0.84[YRI][hapmap]
rs7672426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7674091	0.85[EUR][1000 genomes]
rs7674895	0.85[EUR][1000 genomes]
rs7680416	0.84[YRI][hapmap]
rs7685281	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994679	0.88[MKK][hapmap];0.82[YRI][hapmap]
rs9995112	0.84[YRI][hapmap]
rs9996316	0.84[YRI][hapmap]
rs9996400	0.84[YRI][hapmap]
rs9997898	1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap]
rs9998466	0.83[YRI][hapmap]
rs9998594	0.84[YRI][hapmap]
rs9998776	0.84[YRI][hapmap]

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	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
11	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv593205	chr4:601791-623629	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:593600-605800	Weak transcription	Right Atrium	heart
2	chr4:594800-604200	Weak transcription	Brain Anterior Caudate	brain

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