Variant report

Variant	rs10739390
Chromosome Location	chr9:115988489-115988490
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	chr9:115983573..115985886-chr9:115986006..115988568,3	MCF-7	breast:
2	chr9:115988089..115990143-chr9:115997118..115999123,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136868	Chromatin interaction
ENSG00000119321	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10123415	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125992	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739388	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739392	0.85[EUR][1000 genomes]
rs10759633	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759636	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759637	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759638	0.87[CHB][hapmap]
rs10817461	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817468	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981704	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs10981715	0.87[CHB][hapmap]
rs11789755	0.87[CHB][hapmap]
rs11792628	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12343629	0.87[CHB][hapmap]
rs2296073	0.82[CHB][hapmap]
rs3750532	0.86[CHB][hapmap]
rs3750533	0.87[CHB][hapmap]
rs3750534	0.87[CHB][hapmap]
rs4129395	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129396	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129397	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4284098	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4560868	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979231	0.87[CHB][hapmap]
rs6477998	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477999	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7022397	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7038769	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7041615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859354	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9299214	0.82[CHB][hapmap]

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	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv893746	chr9:115983540-116022826	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10739390	CDC26	cis	Esophagus Muscularis	GTEx
rs10739390	CDC26	cis	Heart Left Ventricle	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115984800-115994800	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr9:115984800-115995400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:115985000-115990200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr9:115985000-115994600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:115985000-115994600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:115985000-115994800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:115985000-115994800	Weak transcription	Left Ventricle	heart
8	chr9:115985000-115996200	Weak transcription	Brain Substantia Nigra	brain
9	chr9:115985000-116020800	Weak transcription	Aorta	Aorta
10	chr9:115985200-115988800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:115985200-115988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:115985200-115988800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:115985200-115989000	Weak transcription	Fetal Kidney	kidney
14	chr9:115985200-115989200	Weak transcription	Brain Anterior Caudate	brain
15	chr9:115985200-115989600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:115985200-115989600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:115985200-115990000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:115985200-115990200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr9:115985200-115990400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:115985200-115991200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr9:115985200-115991600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:115985200-115992200	Weak transcription	Fetal Brain Female	brain
23	chr9:115985200-115992400	Weak transcription	Brain Angular Gyrus	brain
24	chr9:115985200-115992600	Weak transcription	Lung	lung
25	chr9:115985200-115992800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:115985200-115994000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:115985200-115994200	Weak transcription	Fetal Brain Male	brain
28	chr9:115985200-115994600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr9:115985200-115994800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr9:115985200-115998000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:115985200-116001800	Weak transcription	Pancreas	Pancrea
32	chr9:115985400-115989600	Weak transcription	Primary B cells from cord blood	blood
33	chr9:115985400-115989800	Weak transcription	Primary T cells from cord blood	blood
34	chr9:115985400-115994400	Weak transcription	HUVEC	blood vessel
35	chr9:115985400-115995000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr9:115985400-115995600	Weak transcription	HSMMtube	muscle
37	chr9:115985600-115988800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:115985600-115990400	Weak transcription	Gastric	stomach
39	chr9:115985600-115992200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:115985600-115994600	Weak transcription	NHDF-Ad	bronchial
41	chr9:115985600-115994800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:115985600-115995600	Weak transcription	Brain Hippocampus Middle	brain
43	chr9:115985600-115997600	Weak transcription	Brain Germinal Matrix	brain
44	chr9:115985600-116020800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr9:115985800-115990000	Weak transcription	Stomach Mucosa	stomach
46	chr9:115985800-115990200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:115985800-115990400	Weak transcription	Fetal Intestine Small	intestine
48	chr9:115985800-115990400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr9:115985800-115990400	Weak transcription	Small Intestine	intestine
50	chr9:115985800-115994800	Weak transcription	Placenta	Placenta

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