Variant report

Variant	rs3739521
Chromosome Location	chr9:79311892-79311893
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	MAFK	chr9:79311798-79312090	HepG2	liver:	n/a	chr9:79311945-79311960
2	MAFF	chr9:79311820-79312068	HepG2	liver:	n/a	chr9:79311944-79311962
3	RAD21	chr9:79311551-79311900	H1-hESC	embryonic stem cell:	n/a	chr9:79311642-79311651
4	MAFK	chr9:79311791-79312072	IMR90	lung:	n/a	chr9:79311945-79311960
5	MAFK	chr9:79311800-79312124	HepG2	liver:	n/a	chr9:79311945-79311960

Variant related genes	Relation type
PRUNE2	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10781370	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10781371	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10869796	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10869797	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10869798	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10869800	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11145010	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11145011	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11145012	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11145017	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11145018	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11145019	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11145021	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11145023	0.81[ASN][1000 genomes]
rs12238013	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1329014	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1974326	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2077181	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2113942	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277155	0.92[CEU][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs3739524	0.92[CEU][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs577993	0.81[JPT][hapmap]
rs626837	0.81[JPT][hapmap]
rs641088	0.81[JPT][hapmap]
rs658548	0.81[JPT][hapmap]
rs683866	0.81[JPT][hapmap]
rs9785303	1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79307400-79315800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:79307400-79317600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:79307600-79312000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:79307600-79312200	Weak transcription	HSMMtube	muscle
6	chr9:79307600-79312400	Weak transcription	Stomach Mucosa	stomach
7	chr9:79307600-79314400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:79307600-79314600	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:79307600-79315800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:79307800-79312400	Weak transcription	HSMM	muscle
11	chr9:79307800-79314400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:79307800-79314800	Weak transcription	Fetal Brain Female	brain
13	chr9:79307800-79316000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:79308000-79314400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:79308000-79315800	Weak transcription	Aorta	Aorta
16	chr9:79308000-79315800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:79308400-79314800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:79308400-79314800	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:79309000-79314400	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:79309000-79314400	Weak transcription	Fetal Thymus	thymus
21	chr9:79309200-79315600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:79309600-79312200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr9:79309600-79312600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr9:79309600-79312800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:79309800-79312000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:79310400-79313000	Strong transcription	Stomach Smooth Muscle	stomach

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