Variant report

Variant	rs4468582
Chromosome Location	chr15:39960581-39960582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:39826320..39827146-chr15:39960376..39961308,5	MCF-7	breast:
2	chr15:39960405..39961195-chr15:40076760..40077309,2	MCF-7	breast:
3	chr15:39921489..39922463-chr15:39960386..39961014,2	MCF-7	breast:
4	chr15:39922048..39922709-chr15:39960306..39961692,3	MCF-7	breast:
5	chr15:39959771..39962008-chr15:40012951..40014930,2	MCF-7	breast:
6	chr15:39920700..39923129-chr15:39958970..39962199,4	MCF-7	breast:
7	chr15:39870612..39877795-chr15:39952369..39962860,18	MCF-7	breast:
8	chr15:39920057..39920589-chr15:39960433..39961124,2	MCF-7	breast:
9	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
10	chr15:39960376..39961266-chr15:40081056..40081843,2	MCF-7	breast:
11	chr15:39890163..39892186-chr15:39958834..39961393,2	MCF-7	breast:
12	chr15:39892943..39897047-chr15:39958260..39961815,3	MCF-7	breast:
13	chr15:38885388..38886106-chr15:39960478..39961288,3	MCF-7	breast:
14	chr15:39930109..39933577-chr15:39957965..39961029,3	MCF-7	breast:
15	chr15:39878927..39880641-chr15:39959246..39961103,2	MCF-7	breast:
16	chr15:39960300..39964337-chr15:39967513..39971099,4	K562	blood:
17	chr15:39888232..39889117-chr15:39960523..39961284,6	MCF-7	breast:
18	chr15:39888267..39889233-chr15:39960437..39961272,3	MCF-7	breast:
19	chr15:39916809..39917658-chr15:39960492..39961308,2	MCF-7	breast:
20	chr15:39826274..39827051-chr15:39960470..39961265,3	MCF-7	breast:
21	chr15:39880858..39882664-chr15:39957984..39960909,2	MCF-7	breast:
22	chr15:39916809..39917704-chr15:39960492..39961308,3	MCF-7	breast:
23	chr15:39920056..39920589-chr15:39960433..39961135,3	MCF-7	breast:
24	chr15:39888268..39889233-chr15:39960410..39961213,3	MCF-7	breast:
25	chr15:39864703..39865547-chr15:39960441..39961378,3	MCF-7	breast:
26	chr15:39920079..39920917-chr15:39960384..39961046,3	MCF-7	breast:
27	chr15:39921577..39922712-chr15:39960446..39961289,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10520139	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs16969468	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs16969721	0.81[YRI][hapmap]
rs1872761	0.83[MKK][hapmap];0.85[YRI][hapmap]
rs4142520	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7168558	0.94[YRI][hapmap];0.94[AFR][1000 genomes]
rs73393229	0.94[AFR][1000 genomes]
rs73393230	0.94[AFR][1000 genomes]
rs73393232	0.94[AFR][1000 genomes]
rs73393237	0.94[AFR][1000 genomes]
rs73393273	0.92[AFR][1000 genomes]
rs8028707	0.94[AFR][1000 genomes]
rs8040412	0.94[YRI][hapmap];0.94[AFR][1000 genomes]
rs937959	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39956800-39961400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:39957200-39961000	Enhancers	HSMMtube	muscle
3	chr15:39957600-39961200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:39958200-39961000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:39959200-39960800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:39959200-39961200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:39959400-39960800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:39959400-39962800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:39959800-39960800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:39959800-39960800	Weak transcription	Fetal Lung	lung
11	chr15:39959800-39960800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:39959800-39961400	Enhancers	Liver	Liver
13	chr15:39959800-39961600	Weak transcription	Aorta	Aorta
14	chr15:39960000-39961200	Weak transcription	Lung	lung
15	chr15:39960000-39961200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:39960000-39961400	Weak transcription	Fetal Kidney	kidney
17	chr15:39960200-39961200	Weak transcription	Spleen	Spleen
18	chr15:39960200-39961400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:39960200-39962400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:39960200-39964400	Weak transcription	HSMM	muscle
21	chr15:39960200-39972600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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