Variant report

Variant	rs6556898
Chromosome Location	chr5:95347786-95347787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10052503	0.89[CEU][hapmap];0.91[CHB][hapmap]
rs10069748	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs10073752	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1021505	0.83[AFR][1000 genomes]
rs10515232	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1057963	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1057964	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs11738945	0.87[JPT][hapmap]
rs11741590	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs11742959	0.87[JPT][hapmap]
rs11744881	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap]
rs1423268	0.83[CHB][hapmap]
rs1423269	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap]
rs1458017	0.83[CHB][hapmap]
rs1458018	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs17085249	0.91[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap]
rs17085333	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs17085428	0.81[JPT][hapmap]
rs1841010	0.83[CHB][hapmap]
rs1862313	0.83[ASN][1000 genomes]
rs2042340	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs2112566	0.84[ASN][1000 genomes]
rs2161318	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap]
rs2270554	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs2348984	0.85[CHB][hapmap]
rs2546199	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap]
rs2548594	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs3734131	0.84[ASN][1000 genomes]
rs3777162	0.89[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.87[TSI][hapmap]
rs3777163	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs3777165	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs3777166	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3777167	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs3777168	0.82[ASN][1000 genomes]
rs3777171	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs3777173	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs3777175	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs3777178	0.91[CHB][hapmap]
rs3777179	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs3777183	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs3777184	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777185	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap]
rs3777188	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap]
rs3777189	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777190	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap]
rs3777193	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3777194	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs3777196	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs3777200	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap]
rs3777204	0.83[CHB][hapmap]
rs3815768	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap]
rs4538631	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4642392	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs56002885	0.83[ASN][1000 genomes]
rs57243277	0.83[ASN][1000 genomes]
rs6556896	0.80[EUR][1000 genomes]
rs6861531	0.91[CHB][hapmap]
rs6881872	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs6883880	0.83[ASN][1000 genomes]
rs6885567	0.83[CHB][hapmap]
rs6889029	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap]
rs7700895	0.91[CHB][hapmap]
rs7705279	0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[TSI][hapmap]
rs7705720	0.84[ASN][1000 genomes]
rs7710422	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7724599	0.89[CEU][hapmap];0.91[CHB][hapmap]
rs889302	0.83[CHB][hapmap]
rs918629	0.87[TSI][hapmap]
rs9314162	0.91[CHB][hapmap];0.81[JPT][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	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv823146	chr5:95300912-95453557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	esv2757121	chr5:95304236-95539536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	esv34203	chr5:95310985-95452324	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv522097	chr5:95347786-95425199	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv522465	chr5:95347786-95425199	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6556898	ELL2	cis	lymphoblastoid	seeQTL
rs6556898	RIOK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95333400-95351600	Weak transcription	Stomach Mucosa	stomach
2	chr5:95333600-95360800	Weak transcription	Pancreas	Pancrea
3	chr5:95342800-95347800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:95343000-95348000	Weak transcription	NHEK	skin
5	chr5:95343000-95348200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:95344800-95348400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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