Variant report

Variant	rs10012461
Chromosome Location	chr4:573421-573422
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:570799..573548-chr4:580234..582794,2	MCF-7	breast:
2	chr4:560447..562765-chr4:571972..574666,2	MCF-7	breast:
3	chr4:564200..566117-chr4:572319..574456,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE6B-1	chr4:571582-574077	NONHSAT094572

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10015198	0.85[EUR][1000 genomes]
rs10018393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[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];0.96[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]
rs28648408	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]
rs28654405	0.85[EUR][1000 genomes]
rs28682363	0.94[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]
rs34698095	0.85[EUR][1000 genomes]
rs34953355	0.85[EUR][1000 genomes]
rs34992186	0.85[EUR][1000 genomes]
rs35006826	0.85[EUR][1000 genomes]
rs35137658	0.85[EUR][1000 genomes]
rs35158410	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	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	0.81[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	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674895	0.94[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: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	esv1815184	chr4:568928-575087	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv1816544	chr4:568928-575087	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:571200-573600	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr4:571800-573800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:571800-574000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:572200-573600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
5	chr4:572200-573800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:572200-574000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
7	chr4:572400-573800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr4:572400-573800	Enhancers	Brain Angular Gyrus	brain
9	chr4:572400-574000	Flanking Bivalent TSS/Enh	HepG2	liver
10	chr4:572800-573600	Weak transcription	Pancreas	Pancrea
11	chr4:572800-574000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
12	chr4:572800-574000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:573200-574000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:573400-573600	Active TSS	Brain Anterior Caudate	brain
15	chr4:573400-573800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
16	chr4:573400-574000	Bivalent Enhancer	Fetal Thymus	thymus

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