Variant report

Variant	rs13189004
Chromosome Location	chr5:43561694-43561695
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	EBF1	chr5:43561533-43561795	GM12878	blood:	n/a	chr5:43561656-43561667
2	EBF1	chr5:43561171-43561854	GM12878	blood:	n/a	chr5:43561656-43561667
3	MAFF	chr5:43561517-43561735	HepG2	liver:	n/a	n/a
4	MAFK	chr5:43561491-43561768	HepG2	liver:	n/a	chr5:43561607-43561622
5	MAFK	chr5:43561434-43561756	HepG2	liver:	n/a	chr5:43561607-43561622
6	POLR2A	chr5:43561499-43561713	K562	blood:	n/a	n/a
7	MAFK	chr5:43561499-43561793	IMR90	lung:	n/a	chr5:43561607-43561622
8	MAFF	chr5:43561245-43561699	K562	blood:	n/a	n/a

Variant related genes	Relation type
PAIP1	TF binding region

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10036954	0.92[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs10038608	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10042992	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10043934	0.82[EUR][1000 genomes]
rs10045455	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10055801	0.96[MEX][hapmap]
rs10057103	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10058558	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10059993	0.96[MEX][hapmap]
rs10061165	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10065689	0.96[MEX][hapmap]
rs10065863	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10074682	0.96[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs10447144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10462051	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1072745	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1072746	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10941640	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11949083	0.96[MEX][hapmap]
rs12332560	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12521249	0.96[MEX][hapmap]
rs12651879	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12652547	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12659369	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13185343	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13360902	0.96[ASN][1000 genomes]
rs1366410	0.96[MEX][hapmap]
rs1389868	0.96[CEU][hapmap]
rs1428640	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2013173	0.80[EUR][1000 genomes]
rs2172763	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34007811	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs35710460	0.86[EUR][1000 genomes]
rs35881272	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36013953	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776423	0.96[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs3806870	1.00[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs4072918	0.96[MEX][hapmap]
rs4072919	0.91[MEX][hapmap]
rs4073848	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4073850	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4073851	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4074777	0.96[MEX][hapmap]
rs4242099	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4308491	0.82[EUR][1000 genomes]
rs4331909	0.86[EUR][1000 genomes]
rs4367306	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4386738	0.96[MEX][hapmap]
rs4415083	0.83[EUR][1000 genomes]
rs4467713	0.96[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4513704	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4535459	0.91[MEX][hapmap]
rs4541663	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4576155	0.85[EUR][1000 genomes]
rs4610465	0.99[ASN][1000 genomes]
rs4866746	0.83[EUR][1000 genomes]
rs4866752	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4866833	0.96[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4991951	0.83[ASN][1000 genomes]
rs55641556	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56400900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57597020	0.88[EUR][1000 genomes]
rs6451692	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap]
rs6451695	0.96[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs6451696	0.96[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs6451698	0.96[CEU][hapmap];0.83[MEX][hapmap]
rs6451703	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6451704	0.81[EUR][1000 genomes]
rs6451706	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6451712	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6451718	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs67466542	0.81[EUR][1000 genomes]
rs67581152	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6860493	0.96[MEX][hapmap]
rs6861704	0.82[EUR][1000 genomes]
rs6862102	0.96[CEU][hapmap]
rs6865217	0.82[EUR][1000 genomes]
rs6870018	0.96[CEU][hapmap]
rs6870783	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6878770	0.96[MEX][hapmap]
rs6883661	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs6884661	0.96[MEX][hapmap]
rs6885679	0.96[MEX][hapmap]
rs6895327	0.96[MEX][hapmap]
rs6896693	0.96[MEX][hapmap]
rs750582	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs750584	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs7701429	0.87[ASN][1000 genomes]
rs7703662	0.88[JPT][hapmap]
rs7708072	0.88[ASN][1000 genomes]
rs7708369	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs7710125	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7710628	0.91[MEX][hapmap]
rs7713479	0.96[MEX][hapmap]
rs7715782	0.95[MEX][hapmap]
rs7717636	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7718627	0.95[MEX][hapmap]
rs7724571	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs7732656	0.96[MEX][hapmap]
rs7734393	0.87[EUR][1000 genomes]
rs7735243	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7737793	0.99[ASN][1000 genomes]
rs9292883	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9687341	0.82[EUR][1000 genomes]
rs9885467	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	esv1835614	chr5:43515280-43561759	Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	esv1837000	chr5:43515280-43561759	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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
6	esv3471239	chr5:43541792-43587904	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	esv3471240	chr5:43541792-43587904	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	esv1792602	chr5:43556410-43561759	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	45 gene(s)	inside rSNPs	diseases
9	esv1802364	chr5:43556410-43561759	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13189004	MGC42105	cis	lymphoblastoid	seeQTL
rs13189004	YY2	trans	cerebellum	SCAN
rs13189004	C5orf34	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43557800-43563400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:43557800-43563400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:43557800-43571400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr5:43557800-43584600	Weak transcription	Psoas Muscle	Psoas
5	chr5:43558000-43561800	Enhancers	GM12878-XiMat	blood
6	chr5:43558000-43563400	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:43558000-43563400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:43559200-43562800	Enhancers	NHDF-Ad	bronchial
9	chr5:43559600-43562600	Enhancers	Fetal Heart	heart
10	chr5:43559800-43562200	Enhancers	Osteobl	bone
11	chr5:43559800-43562800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:43560200-43562800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:43560200-43584400	Weak transcription	K562	blood
14	chr5:43560600-43562200	Weak transcription	Hela-S3	cervix
15	chr5:43560800-43562400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:43561000-43562000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:43561000-43562000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:43561000-43562200	Enhancers	HSMM	muscle
19	chr5:43561000-43564600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:43561200-43565400	Weak transcription	HepG2	liver
21	chr5:43561600-43562000	Enhancers	HSMMtube	muscle
22	chr5:43561600-43562000	Weak transcription	NHLF	lung

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