Variant report

Variant	rs10940648
Chromosome Location	chr5:59065430-59065431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr5:59065372-59066030	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr5:59063629-59065972	MCF10A-Er-Src	breast:	n/a	chr5:59064369-59064378
3	POLR2A	chr5:59060956-59066265	MCF10A-Er-Src	breast:	n/a	n/a
4	TBP	chr5:59062014-59066021	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:59059243-59065851	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:59060717-59070261	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10514856	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10940647	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11741470	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11747378	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs13164391	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13168643	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs13177163	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13186779	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs159612	1.00[ASW][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap]
rs159614	1.00[ASW][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap]
rs159621	0.80[MEX][hapmap]
rs159625	0.80[MEX][hapmap]
rs17742447	0.81[TSI][hapmap]
rs2938781	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs2938782	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2938787	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs2963820	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs2963823	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs298023	1.00[LWK][hapmap]
rs298056	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs298069	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs298087	1.00[ASW][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs298101	0.81[TSI][hapmap]
rs3111174	1.00[ASW][hapmap];1.00[CHD][hapmap]
rs35302677	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35339176	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35526661	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59251157	0.88[EUR][1000 genomes]
rs62370530	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs877744	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9292210	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59061800-59065600	Active TSS	Hela-S3	cervix
2	chr5:59063000-59065800	Active TSS	HMEC	breast
3	chr5:59064600-59065600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:59064800-59067600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:59064800-59067800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:59065000-59065600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr5:59065000-59065600	Bivalent Enhancer	Osteobl	bone
8	chr5:59065000-59065800	Enhancers	HSMM	muscle
9	chr5:59065200-59065600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
10	chr5:59065200-59065600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
11	chr5:59065200-59065600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:59065200-59065600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:59065200-59065600	Enhancers	Brain Germinal Matrix	brain
14	chr5:59065200-59065600	Enhancers	Fetal Kidney	kidney
15	chr5:59065200-59065600	Enhancers	Fetal Lung	lung
16	chr5:59065200-59065600	Enhancers	Rectal Smooth Muscle	rectum
17	chr5:59065200-59065800	Enhancers	HepG2	liver
18	chr5:59065200-59066000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:59065200-59066000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:59065200-59066000	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr5:59065200-59066000	Flanking Active TSS	A549	lung
22	chr5:59065200-59066200	Enhancers	NH-A	brain
23	chr5:59065200-59066400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr5:59065200-59067600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:59065200-59068000	Weak transcription	Stomach Mucosa	stomach
26	chr5:59065200-59072800	Weak transcription	Aorta	Aorta
27	chr5:59065400-59065600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
28	chr5:59065400-59065600	Enhancers	Colon Smooth Muscle	Colon
29	chr5:59065400-59065600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr5:59065400-59065800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:59065400-59065800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:59065400-59065800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:59065400-59066000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:59065400-59066000	Flanking Active TSS	NHEK	skin
35	chr5:59065400-59066400	Enhancers	HUVEC	blood vessel

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