Variant report

Variant	rs665728
Chromosome Location	chr6:4079875-4079876
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	chr6:4076386..4078865-chr6:4079874..4083762,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-4	chr6:4079440-4079914	NR_104464
2	lnc-C6orf201-4	chr6:4076360-4079955	NONHSAT107293

Variant related genes	Relation type
ENSG00000252668	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs101418	1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs11755877	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs1204951	0.93[ASN][1000 genomes]
rs2326408	0.85[ASN][1000 genomes]
rs2473597	0.93[ASN][1000 genomes]
rs2745453	0.93[ASN][1000 genomes]
rs2745455	0.94[ASN][1000 genomes]
rs2783063	1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[ASN][1000 genomes]
rs2783073	0.85[ASN][1000 genomes]
rs584585	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs588158	0.89[ASN][1000 genomes]
rs589494	0.90[ASN][1000 genomes]
rs590675	0.93[ASN][1000 genomes]
rs592953	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs593291	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[ASN][1000 genomes]
rs594662	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs595413	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs608195	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs609946	0.93[ASN][1000 genomes]
rs611500	0.85[ASN][1000 genomes]
rs612022	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs612477	0.91[ASN][1000 genomes]
rs613028	0.86[ASN][1000 genomes]
rs613260	0.85[ASN][1000 genomes]
rs613709	0.85[ASN][1000 genomes]
rs617604	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617790	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs619439	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs619483	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs619873	0.85[ASN][1000 genomes]
rs620484	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs620901	0.92[ASN][1000 genomes]
rs626080	0.80[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs627259	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs629362	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs633290	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs634114	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[ASN][1000 genomes]
rs634698	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs639905	1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs643232	0.87[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs648900	0.85[ASN][1000 genomes]
rs649725	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs651246	0.93[ASN][1000 genomes]
rs653431	0.93[ASN][1000 genomes]
rs654621	1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs654982	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs659025	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs659305	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs660560	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs661404	0.93[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs661657	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs662834	1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs664299	0.83[ASN][1000 genomes]
rs664839	0.94[ASN][1000 genomes]
rs665894	0.93[ASN][1000 genomes]
rs666254	1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs668070	0.89[ASN][1000 genomes]
rs670932	0.93[ASN][1000 genomes]
rs671364	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs674543	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs676683	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs682063	0.85[MEX][hapmap]
rs688176	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs689308	0.85[ASN][1000 genomes]
rs694903	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs707991	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7166	0.85[ASN][1000 genomes]
rs7744628	0.93[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs7756630	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7757606	0.85[ASN][1000 genomes]
rs853416	0.93[CHB][hapmap];0.85[ASN][1000 genomes]
rs853417	0.85[ASN][1000 genomes]
rs9328220	0.80[CHB][hapmap];0.85[ASN][1000 genomes]
rs9378395	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9405219	0.93[ASN][1000 genomes]
rs942475	1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]

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	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	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	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
7	esv3444323	chr6:4078453-4080526	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4067000-4082400	Weak transcription	Brain Germinal Matrix	brain
2	chr6:4074400-4083000	Weak transcription	Pancreas	Pancrea
3	chr6:4078200-4084600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:4079000-4082400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:4079200-4080000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:4079400-4092000	Weak transcription	Right Atrium	heart

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