Variant report

Variant	rs3806808
Chromosome Location	chr4:120551085-120551086
allele	G/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	CEBPB	chr4:120550924-120551180	HepG2	liver:	n/a	chr4:120551030-120551041 chr4:120550981-120550994 chr4:120551032-120551041
2	CEBPB	chr4:120550860-120551544	IMR90	lung:	n/a	chr4:120551030-120551041 chr4:120550981-120550994 chr4:120551032-120551041
3	CEBPB	chr4:120550949-120551147	A549	lung:	n/a	chr4:120551030-120551041 chr4:120550981-120550994 chr4:120551032-120551041

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120550305..120551270-chr4:120977378..120978356,2	MCF-7	breast:
2	chr4:120550452..120551201-chr4:120970722..120971578,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC110373.1-9	chr4:120548945-120551908	NONHSAT098098

Variant related genes	Relation type
PDE5A	TF binding region

Extended variants
information (count: 133 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10006525	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs10006706	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs10009566	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10009626	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10012252	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10013305	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs10017335	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs10018280	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10019674	0.80[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs10022185	0.84[ASN][1000 genomes]
rs10030660	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10031483	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10050092	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1010739	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1010740	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs10518328	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs10518329	0.86[JPT][hapmap];0.81[TSI][hapmap]
rs10518336	0.91[CHB][hapmap]
rs11098530	0.80[CEU][hapmap]
rs11098531	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11098534	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1155576	0.80[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs11723090	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11729521	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs11731756	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11734241	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs11737395	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs11933966	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11935596	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11947234	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12498599	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs12499377	0.86[EUR][1000 genomes]
rs12502423	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs12504773	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12505735	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12507964	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12508504	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs12510138	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs12512646	0.80[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs12642411	0.84[ASN][1000 genomes]
rs13101722	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13104219	0.85[JPT][hapmap]
rs13122709	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13128602	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs13134665	0.80[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs13136462	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13140391	0.81[EUR][1000 genomes]
rs13140409	0.81[EUR][1000 genomes]
rs13149407	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs1383532	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs1480931	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs1480936	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs1480940	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs1552092	0.90[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs1552095	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs17006190	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs17050695	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs17051352	0.83[ASN][1000 genomes]
rs2127821	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2127823	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs2170276	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2291185	0.80[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs2306456	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2389803	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs2389809	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2389874	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2389879	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2389880	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389882	0.84[ASN][1000 genomes]
rs2389885	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389886	0.84[ASN][1000 genomes]
rs2389887	0.84[ASN][1000 genomes]
rs28394116	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28535956	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28578366	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28787668	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28850368	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2892848	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap]
rs34278750	0.84[ASN][1000 genomes]
rs34835603	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733519	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs3733520	0.80[CEU][hapmap]
rs3733524	0.80[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs3736115	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs3756156	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3775841	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs3775843	0.80[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3775844	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3775845	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3775848	0.80[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3775852	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3822192	0.80[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs3822194	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3822195	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs4504231	0.86[EUR][1000 genomes]
rs4833624	0.80[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs58583086	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59867181	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6534139	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs6534149	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6829903	0.82[EUR][1000 genomes]
rs6832740	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6833334	0.81[EUR][1000 genomes]
rs6834796	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs6835635	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs6848389	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs6849171	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6849561	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs6853998	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6855918	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7659501	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7664440	0.84[ASN][1000 genomes]
rs7665125	0.86[JPT][hapmap]
rs7669520	0.82[EUR][1000 genomes]
rs7671096	0.83[ASN][1000 genomes]
rs7676296	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7680914	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7681544	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7687843	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7688802	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7692994	0.83[JPT][hapmap]
rs7693919	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7695292	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7695620	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7699064	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs9884402	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs9997631	0.82[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap]
rs9998585	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3806808	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs3806808	RP11-33B1.1	cis	lung	GTEx
rs3806808	RP11-33B1.1	cis	Whole Blood	GTEx
rs3806808	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs3806808	C4orf3	cis	cerebellum	SCAN
rs3806808	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs3806808	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs3806808	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120550400-120551400	Flanking Active TSS	Osteobl	bone
2	chr4:120550600-120551200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:120550600-120551200	Enhancers	Brain Hippocampus Middle	brain
4	chr4:120550600-120551200	Flanking Active TSS	Colon Smooth Muscle	Colon
5	chr4:120550600-120553600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:120550600-120554400	Weak transcription	Pancreas	Pancrea
7	chr4:120550800-120551200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr4:120550800-120551200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:120550800-120551200	Enhancers	Fetal Kidney	kidney
10	chr4:120550800-120551400	Bivalent Enhancer	Primary T cells from cord blood	blood
11	chr4:120550800-120551600	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr4:120550800-120552000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:120550800-120552600	Enhancers	Rectal Smooth Muscle	rectum
14	chr4:120550800-120553200	Weak transcription	NHDF-Ad	bronchial
15	chr4:120550800-120553400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:120550800-120553400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:120550800-120553400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:120550800-120553400	Weak transcription	NH-A	brain
19	chr4:120550800-120553600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:120551000-120551200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:120551000-120551200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr4:120551000-120551600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr4:120551000-120551600	Flanking Active TSS	NHLF	lung
24	chr4:120551000-120552200	Enhancers	Fetal Lung	lung
25	chr4:120551000-120552400	Enhancers	Fetal Stomach	stomach
26	chr4:120551000-120553400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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