Variant report

Variant	rs3909931
Chromosome Location	chr5:106793983-106793984
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	chr5:106775777..106777698-chr5:106792943..106795923,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12523318	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13182976	0.82[TSI][hapmap]
rs153114	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs153133	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17533525	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1835111	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797517	0.86[TSI][hapmap]
rs3901010	0.85[EUR][1000 genomes]
rs526521	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs537500	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868410	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv462379	chr5:106789764-106806438	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv471037	chr5:106789764-106806438	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv599334	chr5:106789764-106806438	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106789600-106800000	Weak transcription	Aorta	Aorta
2	chr5:106790600-106794000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr5:106790600-106794000	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr5:106790600-106794000	Enhancers	GM12878-XiMat	blood
5	chr5:106790600-106794400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr5:106790800-106795400	Weak transcription	Right Ventricle	heart
7	chr5:106791000-106801400	Weak transcription	Right Atrium	heart
8	chr5:106791400-106794400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:106791600-106795600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:106791800-106795400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:106792000-106794000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:106792200-106796600	Enhancers	A549	lung
13	chr5:106792600-106800000	Weak transcription	Fetal Lung	lung
14	chr5:106792600-106800200	Weak transcription	Fetal Stomach	stomach
15	chr5:106792600-106801600	Weak transcription	HSMM	muscle
16	chr5:106792800-106795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:106792800-106796400	Weak transcription	Fetal Kidney	kidney
18	chr5:106792800-106799800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:106792800-106801000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:106792800-106804800	Weak transcription	Esophagus	oesophagus
21	chr5:106793000-106794000	Weak transcription	Stomach Mucosa	stomach
22	chr5:106793000-106796000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:106793000-106796400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:106793200-106794800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:106793200-106795400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:106793200-106796000	Weak transcription	HMEC	breast
27	chr5:106793200-106796000	Weak transcription	NHEK	skin
28	chr5:106793200-106796400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:106793200-106796400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:106793200-106796400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:106793200-106797000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:106793200-106797600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:106793400-106794200	Enhancers	Duodenum Mucosa	Duodenum
34	chr5:106793400-106794600	Enhancers	Fetal Heart	heart
35	chr5:106793600-106795400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:106793800-106795000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr5:106793800-106795400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:106793800-106796600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:106793800-106799600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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