Variant report

Variant	rs4974601
Chromosome Location	chr4:1095410-1095411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10084890	0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs1010342	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10902752	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs11247973	0.90[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732520	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11939380	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11940546	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12645644	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs12647929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13107058	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs13135215	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs13146371	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1453605	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1466214	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1466215	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1670533	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1670534	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs17164380	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs1825093	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2014318	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2045065	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs2045066	0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs2100411	0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2290408	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2290409	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28620427	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35366709	0.94[ASN][1000 genomes]
rs3796619	1.00[ASW][hapmap];1.00[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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796620	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4045481	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4690209	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4690212	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs4690213	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs4690214	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs4974638	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55741287	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585735	0.87[ASN][1000 genomes]
rs604597	0.96[ASN][1000 genomes]
rs610218	0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs62294748	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62294756	0.94[ASN][1000 genomes]
rs629260	0.92[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs633556	0.96[ASN][1000 genomes]
rs641987	0.86[ASN][1000 genomes]
rs643484	0.89[ASN][1000 genomes]
rs651017	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs652063	0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6599276	0.94[CHB][hapmap];0.91[JPT][hapmap]
rs676561	0.90[ASN][1000 genomes]
rs6812586	0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6812596	0.94[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6822863	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs6827206	0.82[ASN][1000 genomes]
rs6835141	0.84[ASN][1000 genomes]
rs6836350	0.94[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6837145	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6839931	0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs6852850	0.94[CHB][hapmap];0.91[JPT][hapmap]
rs6854793	0.94[CHB][hapmap];0.91[JPT][hapmap]
rs6857085	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs688008	0.90[ASN][1000 genomes]
rs688785	0.90[ASN][1000 genomes]
rs7660779	0.84[ASN][1000 genomes]
rs7673898	0.88[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1003219	chr4:769894-1105464	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv536980	chr4:827866-1167377	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv1004727	chr4:1015652-1158207	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv536984	chr4:1015652-1158207	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv1005990	chr4:1015652-1167619	Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv1000594	chr4:1045099-1129975	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1001165	chr4:1051512-1129975	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4974601	ZFYVE28	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1086000-1098400	Weak transcription	Lung	lung
2	chr4:1086200-1098600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:1093800-1098000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:1093800-1098000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:1094000-1105800	Weak transcription	Ovary	ovary
6	chr4:1094600-1098000	Weak transcription	Pancreas	Pancrea

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