Variant report

Variant	rs28648408
Chromosome Location	chr4:575535-575536
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:517866..521551-chr4:574619..578020,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE6B-1	chr4:574545-576019	NONHSAT094577

Variant related genes	Relation type
ENSG00000174227	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10012461	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015198	1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10018393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10024575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101691	0.85[EUR][1000 genomes]
rs13103955	0.85[EUR][1000 genomes]
rs13107526	0.85[EUR][1000 genomes]
rs13111179	0.85[EUR][1000 genomes]
rs13116523	0.85[EUR][1000 genomes]
rs13117283	0.85[EUR][1000 genomes]
rs13127213	0.89[EUR][1000 genomes]
rs13133935	0.85[EUR][1000 genomes]
rs13136626	0.85[EUR][1000 genomes]
rs13139052	0.82[EUR][1000 genomes]
rs13139089	0.85[EUR][1000 genomes]
rs13147797	0.85[EUR][1000 genomes]
rs13150119	0.85[EUR][1000 genomes]
rs28654405	0.85[EUR][1000 genomes]
rs28682363	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28687729	0.85[EUR][1000 genomes]
rs28710261	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28754934	0.85[EUR][1000 genomes]
rs34053163	0.85[EUR][1000 genomes]
rs34075612	0.85[EUR][1000 genomes]
rs34094325	0.85[EUR][1000 genomes]
rs34096984	0.85[EUR][1000 genomes]
rs34165278	0.85[EUR][1000 genomes]
rs34293668	0.85[EUR][1000 genomes]
rs34363025	0.85[EUR][1000 genomes]
rs34366493	0.85[EUR][1000 genomes]
rs34391278	0.85[EUR][1000 genomes]
rs34402770	0.85[EUR][1000 genomes]
rs34421911	0.85[EUR][1000 genomes]
rs34477049	0.85[EUR][1000 genomes]
rs34568772	0.85[EUR][1000 genomes]
rs34585712	0.85[EUR][1000 genomes]
rs34587191	1.00[TSI][hapmap]
rs34698095	0.85[EUR][1000 genomes]
rs34953355	1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs34992186	0.85[EUR][1000 genomes]
rs35006826	0.85[EUR][1000 genomes]
rs35137658	0.85[EUR][1000 genomes]
rs35158410	1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs35207129	0.85[EUR][1000 genomes]
rs35219160	0.85[EUR][1000 genomes]
rs35270524	0.85[EUR][1000 genomes]
rs35455427	0.85[EUR][1000 genomes]
rs35535457	0.85[EUR][1000 genomes]
rs35564967	0.85[EUR][1000 genomes]
rs35621580	0.85[EUR][1000 genomes]
rs35649145	1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs35694609	0.85[EUR][1000 genomes]
rs35732782	0.85[EUR][1000 genomes]
rs35843044	0.85[EUR][1000 genomes]
rs35853545	0.85[EUR][1000 genomes]
rs35869797	0.85[EUR][1000 genomes]
rs35894204	0.85[EUR][1000 genomes]
rs35896648	0.85[EUR][1000 genomes]
rs35935310	0.85[EUR][1000 genomes]
rs35972513	0.85[EUR][1000 genomes]
rs36060793	0.85[EUR][1000 genomes]
rs36117387	0.85[EUR][1000 genomes]
rs4420926	0.94[ASN][1000 genomes]
rs56291707	0.88[ASN][1000 genomes]
rs57138956	1.00[ASN][1000 genomes]
rs57161616	1.00[ASN][1000 genomes]
rs57794368	1.00[ASN][1000 genomes]
rs59921252	1.00[ASN][1000 genomes]
rs6838555	1.00[JPT][hapmap]
rs71602477	0.85[EUR][1000 genomes]
rs71602479	0.85[EUR][1000 genomes]
rs71602480	0.85[EUR][1000 genomes]
rs71602481	0.85[EUR][1000 genomes]
rs71602482	0.85[EUR][1000 genomes]
rs71602484	0.85[EUR][1000 genomes]
rs71602486	0.85[EUR][1000 genomes]
rs71602489	0.85[EUR][1000 genomes]
rs71602492	0.85[EUR][1000 genomes]
rs73056528	1.00[ASN][1000 genomes]
rs73056535	1.00[ASN][1000 genomes]
rs73056537	1.00[ASN][1000 genomes]
rs73074224	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73074226	1.00[ASN][1000 genomes]
rs73074229	1.00[ASN][1000 genomes]
rs7657809	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672426	0.85[EUR][1000 genomes]
rs7674091	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674895	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685281	0.85[EUR][1000 genomes]

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	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

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:574800-575600	Flanking Active TSS	HepG2	liver
2	chr4:574800-576000	Enhancers	Brain Cingulate Gyrus	brain
3	chr4:575000-575600	Enhancers	Brain Anterior Caudate	brain
4	chr4:575200-576000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:575200-576000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:575400-575600	Bivalent Enhancer	Brain Hippocampus Middle	brain
7	chr4:575400-575600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
8	chr4:575400-575800	Enhancers	Brain Angular Gyrus	brain

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