Variant report

Variant	rs626080
Chromosome Location	chr6:4101567-4101568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4101330..4103030-chr6:4105237..4107342,2	K562	blood:
2	chr6:4101330..4103271-chr6:4104931..4106737,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-4	chr6:4100714-4102618	ucscGeneNc_uc003mwg_1
2	lnc-C6orf201-4	chr6:4100799-4103637	NONHSAT107304
3	lnc-C6orf201-4	chr6:4101545-4101595	NONHSAT107297

Extended variants
information (count: 97 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs101418	0.84[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs11755877	0.84[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs1204951	0.93[ASN][1000 genomes]
rs2326408	0.97[ASN][1000 genomes]
rs2473597	0.86[ASN][1000 genomes]
rs2745453	0.86[ASN][1000 genomes]
rs2745455	0.91[ASN][1000 genomes]
rs2783063	0.84[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2783073	0.97[ASN][1000 genomes]
rs28878015	0.88[ASN][1000 genomes]
rs4959271	0.86[ASN][1000 genomes]
rs582008	0.85[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs583782	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs583881	0.80[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs584585	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs590675	0.86[ASN][1000 genomes]
rs592953	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs593291	0.84[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs594662	0.84[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs595413	0.84[CHB][hapmap];0.85[CHD][hapmap];0.86[ASN][1000 genomes]
rs608195	0.84[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.82[MKK][hapmap];0.95[ASN][1000 genomes]
rs609946	0.86[ASN][1000 genomes]
rs611500	0.97[ASN][1000 genomes]
rs612022	0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs612477	0.95[ASN][1000 genomes]
rs613028	0.99[ASN][1000 genomes]
rs613260	0.97[ASN][1000 genomes]
rs613709	0.97[ASN][1000 genomes]
rs617604	0.91[ASN][1000 genomes]
rs617790	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs619439	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs619483	0.84[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs619873	0.97[ASN][1000 genomes]
rs620484	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs620901	0.84[ASN][1000 genomes]
rs621205	0.87[ASN][1000 genomes]
rs627259	0.95[ASN][1000 genomes]
rs629362	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs633290	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs634114	0.84[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs634698	0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs634970	0.81[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs638329	0.85[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs639905	0.84[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs643232	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs646385	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs648900	0.97[ASN][1000 genomes]
rs649725	0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs651246	0.86[ASN][1000 genomes]
rs653431	0.86[ASN][1000 genomes]
rs654621	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs654982	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs659025	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs659051	0.88[ASN][1000 genomes]
rs659305	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs660560	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs660957	0.88[ASN][1000 genomes]
rs661404	0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs661657	0.93[ASN][1000 genomes]
rs662834	0.84[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs664299	0.95[ASN][1000 genomes]
rs664635	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs664839	0.84[ASN][1000 genomes]
rs664898	0.88[ASN][1000 genomes]
rs665728	0.80[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs665894	0.91[ASN][1000 genomes]
rs666254	0.84[CHB][hapmap];0.88[ASN][1000 genomes]
rs668070	0.89[ASN][1000 genomes]
rs670932	0.86[ASN][1000 genomes]
rs671364	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs674543	0.91[ASN][1000 genomes]
rs676683	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs678285	0.81[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs679303	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs688176	0.84[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs689308	0.97[ASN][1000 genomes]
rs694058	0.88[ASN][1000 genomes]
rs694903	0.95[ASN][1000 genomes]
rs707991	0.84[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7166	0.85[CHD][hapmap];0.97[ASN][1000 genomes]
rs7744628	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7756630	0.82[ASN][1000 genomes]
rs7757606	0.97[ASN][1000 genomes]
rs853416	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs853417	0.97[ASN][1000 genomes]
rs853418	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9328220	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9378395	0.84[ASN][1000 genomes]
rs9405219	0.91[ASN][1000 genomes]
rs9405701	0.88[ASN][1000 genomes]
rs942475	0.84[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs626080	FOXF2	cis	cerebellum	SCAN
rs626080	PECI	cis	cerebellum	SCAN
rs626080	PECI	cis	parietal	SCAN
rs626080	HUS1B	cis	parietal	SCAN
rs626080	PECI	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4090800-4103000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:4092600-4103000	Weak transcription	Pancreas	Pancrea
3	chr6:4100800-4104400	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr6:4101000-4101800	Enhancers	Gastric	stomach
5	chr6:4101000-4102000	Enhancers	Psoas Muscle	Psoas
6	chr6:4101000-4102800	Enhancers	HepG2	liver
7	chr6:4101000-4103400	Enhancers	Skeletal Muscle Female	skeletal muscle

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