Variant report

Variant	rs13139089
Chromosome Location	chr4:626028-626029
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:626004..628523-chr4:666543..668678,2	K562	blood:
2	chr4:619501..622132-chr4:622263..626030,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169020	Chromatin interaction
ENSG00000215375	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10012461	0.85[EUR][1000 genomes]
rs10015198	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10018393	0.85[EUR][1000 genomes]
rs10024575	0.85[EUR][1000 genomes]
rs13101691	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13103955	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13104878	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13107526	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13110755	0.87[EUR][1000 genomes]
rs13111179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13114299	0.87[EUR][1000 genomes]
rs13116523	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13117283	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13118033	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13127213	0.96[EUR][1000 genomes]
rs13133935	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13136626	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13139052	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13143415	0.91[EUR][1000 genomes]
rs13147797	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13150119	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648408	0.85[EUR][1000 genomes]
rs28654405	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28682363	0.85[EUR][1000 genomes]
rs28687729	1.00[EUR][1000 genomes]
rs28754934	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34053163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34075612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34094325	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34096984	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34165278	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34293668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34363025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34366493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34391278	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34402770	1.00[EUR][1000 genomes]
rs34421911	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34477049	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34568772	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34585712	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34587191	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34698095	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34953355	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34992186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35006826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35137658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35158410	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35207129	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35219160	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35270524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35455427	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35535457	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35564967	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35621318	0.87[EUR][1000 genomes]
rs35621580	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35649145	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35694609	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35732782	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35843044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35853545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35869797	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35894204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35896648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35925646	0.87[EUR][1000 genomes]
rs35935310	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35972513	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36060793	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36117387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61760239	0.87[EUR][1000 genomes]
rs71602477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602479	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602486	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602489	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602490	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71602492	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602500	0.87[EUR][1000 genomes]
rs7657809	0.85[EUR][1000 genomes]
rs7672426	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7674091	0.85[EUR][1000 genomes]
rs7674895	0.85[EUR][1000 genomes]
rs7685281	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
15	esv993737	chr4:618112-628837	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	esv3340754	chr4:623752-628150	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	esv3438877	chr4:625002-627800	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:624600-630400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:625600-626600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
3	chr4:625600-627400	ZNF genes & repeats	Spleen	Spleen
4	chr4:626000-626400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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